https://launchpad.net/ubuntu/+source/khmer/2.1.2+dfsg-11/+build/24304739 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-008 5.4.0-124-generic #140-Ubuntu SMP Thu Aug 4 02:27:01 UTC 2022 aarch64 Buildd toolchain package versions: launchpad-buildd_219~583~ubuntu20.04.1 python3-lpbuildd_219~583~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.5 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 22 Aug 21:49:48 ntpdate[1922]: adjust time server 10.211.37.1 offset 0.007741 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=kinetic --arch=arm64 PACKAGEBUILD-24304739 --image-type chroot /home/buildd/filecache-default/46a86ed06ad4eec780192fe4231116bc064b7a44 Creating target for build PACKAGEBUILD-24304739 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=kinetic --arch=arm64 PACKAGEBUILD-24304739 Starting target for build PACKAGEBUILD-24304739 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=kinetic --arch=arm64 PACKAGEBUILD-24304739 'deb http://ftpmaster.internal/ubuntu kinetic main universe' 'deb http://ftpmaster.internal/ubuntu kinetic-security main universe' 'deb http://ftpmaster.internal/ubuntu kinetic-updates main universe' 'deb http://ftpmaster.internal/ubuntu kinetic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-24304739 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=kinetic --arch=arm64 PACKAGEBUILD-24304739 Updating target for build PACKAGEBUILD-24304739 Get:1 http://ftpmaster.internal/ubuntu kinetic InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic/main arm64 Packages [1380 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/universe arm64 Packages [14.2 MB] Get:8 http://ftpmaster.internal/ubuntu kinetic/universe Translation-en [5792 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 Packages [171 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic-proposed/main Translation-en [50.9 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic-proposed/universe arm64 Packages [591 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic-proposed/universe Translation-en [225 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic-proposed/restricted arm64 Packages [43.0 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic-proposed/restricted Translation-en [16.0 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic-proposed/multiverse arm64 Packages [14.8 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic-proposed/multiverse Translation-en [7792 B] Fetched 23.6 MB in 41s (572 kB/s) Reading package lists... W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (main/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (universe/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (main/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (universe/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: g++-11 libstdc++-11-dev Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: cpp-12 g++-12 gcc-12 libasan8 libfdisk1 libgcc-12-dev libgprofng0 libstdc++-12-dev libtsan2 sgml-base util-linux-extra The following packages will be upgraded: adduser advancecomp apt base-files base-passwd binutils binutils-aarch64-linux-gnu binutils-common bsdutils cpp cpp-11 dash debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils g++ g++-11 gcc gcc-11 gcc-11-base gcc-12-base gpg gpg-agent gpgconf gpgv gzip init init-system-helpers libapparmor1 libapt-pkg6.0 libasan6 libassuan0 libatomic1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdpkg-perl libext2fs2 libfakeroot libgcc-11-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libhogweed6 libhwasan0 libidn2-0 libip4tc2 libisl23 libitm1 libjson-c5 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblsan0 liblzma5 libmount1 libncurses6 libncursesw6 libnettle8 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpcre3 libperl5.34 libpng16-16 libprocps8 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssl3 libstdc++-11-dev libstdc++6 libsystemd0 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login logsave lsb-base lto-disabled-list mawk mount ncurses-base ncurses-bin openssl passwd perl perl-base perl-modules-5.34 pinentry-curses policyrcd-script-zg2 procps readline-common systemd systemd-sysv usrmerge util-linux xz-utils zlib1g 136 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. Need to get 305 MB of archives. After this operation, 721 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu kinetic/main arm64 libcrypt-dev arm64 1:4.4.28-2 [120 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 libc6-dev arm64 2.36-0ubuntu2 [1545 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 libc-dev-bin arm64 2.36-0ubuntu2 [19.5 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic/main arm64 libcrypt1 arm64 1:4.4.28-2 [84.9 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 linux-libc-dev arm64 5.19.0-15.15 [1270 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main arm64 libtirpc-common all 1.3.3+ds-1 [7790 B] Get:7 http://ftpmaster.internal/ubuntu kinetic/main arm64 libk5crypto3 arm64 1.20-1 [85.0 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic/main arm64 libgssapi-krb5-2 arm64 1.20-1 [139 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic/main arm64 libkrb5-3 arm64 1.20-1 [345 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic/main arm64 libkrb5support0 arm64 1.20-1 [31.2 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic/main arm64 libcom-err2 arm64 1.46.5-2ubuntu2 [8868 B] Get:12 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 libkeyutils1 arm64 1.6.3-1 [10.6 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic/main arm64 libssl3 arm64 3.0.5-2ubuntu1 [1752 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic/main arm64 libtirpc-dev arm64 1.3.3+ds-1 [199 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic/main arm64 libtirpc3 arm64 1.3.3+ds-1 [82.1 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 libc6 arm64 2.36-0ubuntu2 [2706 kB] Get:17 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 libc-bin arm64 2.36-0ubuntu2 [591 kB] Get:18 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 libatomic1 arm64 12.1.0-8ubuntu2 [10.7 kB] Get:19 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 libubsan1 arm64 12.1.0-8ubuntu2 [957 kB] Get:20 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 liblsan0 arm64 12.1.0-8ubuntu2 [1027 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 libitm1 arm64 12.1.0-8ubuntu2 [27.9 kB] Get:22 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 libhwasan0 arm64 12.1.0-8ubuntu2 [1109 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 libgomp1 arm64 12.1.0-8ubuntu2 [122 kB] Get:24 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 gcc-12-base arm64 12.1.0-8ubuntu2 [19.3 kB] Get:25 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 libgcc-s1 arm64 12.1.0-8ubuntu2 [39.6 kB] Get:26 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 libcc1-0 arm64 12.1.0-8ubuntu2 [44.1 kB] Get:27 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 libstdc++6 arm64 12.1.0-8ubuntu2 [648 kB] Get:28 http://ftpmaster.internal/ubuntu kinetic/main arm64 base-files arm64 12.2ubuntu2 [73.3 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic/main arm64 bsdutils arm64 1:2.38-4ubuntu1 [83.9 kB] Get:30 http://ftpmaster.internal/ubuntu kinetic/main arm64 debianutils arm64 5.7-0.3 [103 kB] Get:31 http://ftpmaster.internal/ubuntu kinetic/main arm64 libzstd1 arm64 1.5.2+dfsg-1 [249 kB] Get:32 http://ftpmaster.internal/ubuntu kinetic/main arm64 libgpg-error0 arm64 1.45-2 [68.6 kB] Get:33 http://ftpmaster.internal/ubuntu kinetic/main arm64 libgcrypt20 arm64 1.10.1-2ubuntu1 [467 kB] Get:34 http://ftpmaster.internal/ubuntu kinetic/main arm64 liblzma5 arm64 5.2.5-2.1 [97.6 kB] Get:35 http://ftpmaster.internal/ubuntu kinetic/main arm64 libblkid1 arm64 2.38-4ubuntu1 [103 kB] Get:36 http://ftpmaster.internal/ubuntu kinetic/main arm64 libuuid1 arm64 2.38-4ubuntu1 [23.2 kB] Get:37 http://ftpmaster.internal/ubuntu kinetic/main arm64 libfdisk1 arm64 2.38-4ubuntu1 [140 kB] Get:38 http://ftpmaster.internal/ubuntu kinetic/main arm64 systemd-sysv arm64 251.2-2ubuntu2 [11.2 kB] Get:39 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 libapparmor1 arm64 3.0.7-1ubuntu1 [36.6 kB] Get:40 http://ftpmaster.internal/ubuntu kinetic/main arm64 libjson-c5 arm64 0.16-1 [33.2 kB] Get:41 http://ftpmaster.internal/ubuntu kinetic/main arm64 libcryptsetup12 arm64 2:2.5.0-1ubuntu1 [216 kB] Get:42 http://ftpmaster.internal/ubuntu kinetic/main arm64 libip4tc2 arm64 1.8.7-1ubuntu6 [19.6 kB] Get:43 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 libkmod2 arm64 30+20220630-3ubuntu1 [47.1 kB] Get:44 http://ftpmaster.internal/ubuntu kinetic/main arm64 libpcre2-8-0 arm64 10.40-1 [210 kB] Get:45 http://ftpmaster.internal/ubuntu kinetic/main arm64 libselinux1 arm64 3.4-1 [77.2 kB] Get:46 http://ftpmaster.internal/ubuntu kinetic/main arm64 libmount1 arm64 2.38-4ubuntu1 [120 kB] Get:47 http://ftpmaster.internal/ubuntu kinetic/main arm64 libpam0g arm64 1.5.2-2ubuntu1 [60.2 kB] Get:48 http://ftpmaster.internal/ubuntu kinetic/main arm64 libseccomp2 arm64 2.5.4-1ubuntu1 [46.5 kB] Get:49 http://ftpmaster.internal/ubuntu kinetic/main arm64 mount arm64 2.38-4ubuntu1 [113 kB] Get:50 http://ftpmaster.internal/ubuntu kinetic/main arm64 libsemanage-common all 3.4-1 [9828 B] Get:51 http://ftpmaster.internal/ubuntu kinetic/main arm64 libsepol2 arm64 3.4-2 [285 kB] Get:52 http://ftpmaster.internal/ubuntu kinetic/main arm64 libsemanage2 arm64 3.4-1 [89.7 kB] Get:53 http://ftpmaster.internal/ubuntu kinetic/main arm64 libpam-modules-bin arm64 1.5.2-2ubuntu1 [43.4 kB] Get:54 http://ftpmaster.internal/ubuntu kinetic/main arm64 libpam-modules arm64 1.5.2-2ubuntu1 [282 kB] Get:55 http://ftpmaster.internal/ubuntu kinetic/main arm64 passwd arm64 1:4.11.1+dfsg1-2ubuntu1 [765 kB] Get:56 http://ftpmaster.internal/ubuntu kinetic/main arm64 adduser all 3.121ubuntu1 [150 kB] Get:57 http://ftpmaster.internal/ubuntu kinetic/main arm64 systemd arm64 251.2-2ubuntu2 [4550 kB] Get:58 http://ftpmaster.internal/ubuntu kinetic/main arm64 libsystemd0 arm64 251.2-2ubuntu2 [320 kB] Get:59 http://ftpmaster.internal/ubuntu kinetic/main arm64 libudev1 arm64 251.2-2ubuntu2 [80.0 kB] Get:60 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 zlib1g arm64 1:1.2.11.dfsg-4.1ubuntu1 [56.9 kB] Get:61 http://ftpmaster.internal/ubuntu kinetic/main arm64 libapt-pkg6.0 arm64 2.5.2 [859 kB] Get:62 http://ftpmaster.internal/ubuntu kinetic/main arm64 dpkg arm64 1.21.9ubuntu1 [1328 kB] Get:63 http://ftpmaster.internal/ubuntu kinetic/main arm64 dash arm64 0.5.11+git20210903+057cd650a4ed-8ubuntu1 [88.4 kB] Get:64 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 diffutils arm64 1:3.8-1 [169 kB] Get:65 http://ftpmaster.internal/ubuntu kinetic/main arm64 findutils arm64 4.9.0-3ubuntu1 [295 kB] Get:66 http://ftpmaster.internal/ubuntu kinetic/main arm64 gzip arm64 1.12-1ubuntu1 [96.0 kB] Get:67 http://ftpmaster.internal/ubuntu kinetic/main arm64 login arm64 1:4.11.1+dfsg1-2ubuntu1 [183 kB] Get:68 http://ftpmaster.internal/ubuntu kinetic/main arm64 ncurses-bin arm64 6.3+20220423-2 [183 kB] Get:69 http://ftpmaster.internal/ubuntu kinetic/main arm64 libperl5.34 arm64 5.34.0-5ubuntu1 [4613 kB] Get:70 http://ftpmaster.internal/ubuntu kinetic/main arm64 perl arm64 5.34.0-5ubuntu1 [231 kB] Get:71 http://ftpmaster.internal/ubuntu kinetic/main arm64 perl-base arm64 5.34.0-5ubuntu1 [1689 kB] Get:72 http://ftpmaster.internal/ubuntu kinetic/main arm64 perl-modules-5.34 all 5.34.0-5ubuntu1 [2952 kB] Get:73 http://ftpmaster.internal/ubuntu kinetic/main arm64 libdb5.3 arm64 5.3.28+dfsg1-0.10 [710 kB] Get:74 http://ftpmaster.internal/ubuntu kinetic/main arm64 libsmartcols1 arm64 2.38-4ubuntu1 [49.4 kB] Get:75 http://ftpmaster.internal/ubuntu kinetic/main arm64 util-linux-extra arm64 2.38-4ubuntu1 [81.4 kB] Get:76 http://ftpmaster.internal/ubuntu kinetic/main arm64 util-linux arm64 2.38-4ubuntu1 [1069 kB] Get:77 http://ftpmaster.internal/ubuntu kinetic/main arm64 base-passwd arm64 3.6.0 [49.4 kB] Get:78 http://ftpmaster.internal/ubuntu kinetic/main arm64 init-system-helpers all 1.64 [38.7 kB] Get:79 http://ftpmaster.internal/ubuntu kinetic/main arm64 ncurses-base all 6.3+20220423-2 [21.2 kB] Get:80 http://ftpmaster.internal/ubuntu kinetic/main arm64 libnettle8 arm64 3.8.1-2 [182 kB] Get:81 http://ftpmaster.internal/ubuntu kinetic/main arm64 libhogweed6 arm64 3.8.1-2 [197 kB] Get:82 http://ftpmaster.internal/ubuntu kinetic/main arm64 sgml-base all 1.30 [12.5 kB] Get:83 http://ftpmaster.internal/ubuntu kinetic/main arm64 libidn2-0 arm64 2.3.3-1 [63.2 kB] Get:84 http://ftpmaster.internal/ubuntu kinetic/main arm64 libp11-kit0 arm64 0.24.1-1 [232 kB] Get:85 http://ftpmaster.internal/ubuntu kinetic/main arm64 libgnutls30 arm64 3.7.7-2ubuntu1 [931 kB] Get:86 http://ftpmaster.internal/ubuntu kinetic/main arm64 gpgv arm64 2.2.35-3ubuntu1 [132 kB] Get:87 http://ftpmaster.internal/ubuntu kinetic/main arm64 apt arm64 2.5.2 [1343 kB] Get:88 http://ftpmaster.internal/ubuntu kinetic/main arm64 logsave arm64 1.46.5-2ubuntu2 [9768 B] Get:89 http://ftpmaster.internal/ubuntu kinetic/main arm64 libext2fs2 arm64 1.46.5-2ubuntu2 [208 kB] Get:90 http://ftpmaster.internal/ubuntu kinetic/main arm64 e2fsprogs arm64 1.46.5-2ubuntu2 [580 kB] Get:91 http://ftpmaster.internal/ubuntu kinetic/main arm64 init arm64 1.64 [5536 B] Get:92 http://ftpmaster.internal/ubuntu kinetic/main arm64 libcap-ng0 arm64 0.8.3-1 [15.0 kB] Get:93 http://ftpmaster.internal/ubuntu kinetic/main arm64 libpam-runtime all 1.5.2-2ubuntu1 [40.0 kB] Get:94 http://ftpmaster.internal/ubuntu kinetic/main arm64 libpcre3 arm64 2:8.39-14 [231 kB] Get:95 http://ftpmaster.internal/ubuntu kinetic/main arm64 libncurses6 arm64 6.3+20220423-2 [106 kB] Get:96 http://ftpmaster.internal/ubuntu kinetic/main arm64 libncursesw6 arm64 6.3+20220423-2 [140 kB] Get:97 http://ftpmaster.internal/ubuntu kinetic/main arm64 libtinfo6 arm64 6.3+20220423-2 [96.5 kB] Get:98 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 lsb-base all 11.2ubuntu1 [12.4 kB] Get:99 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 libprocps8 arm64 2:3.3.17-7ubuntu1 [34.3 kB] Get:100 http://ftpmaster.internal/ubuntu kinetic/main arm64 libss2 arm64 1.46.5-2ubuntu2 [11.9 kB] Get:101 http://ftpmaster.internal/ubuntu kinetic/main arm64 mawk arm64 1.3.4.20200120-3.1 [106 kB] Get:102 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 procps arm64 2:3.3.17-7ubuntu1 [378 kB] Get:103 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 usrmerge all 29ubuntu1 [55.7 kB] Get:104 http://ftpmaster.internal/ubuntu kinetic/main arm64 readline-common all 8.1.2-1.2 [53.6 kB] Get:105 http://ftpmaster.internal/ubuntu kinetic/main arm64 libreadline8 arm64 8.1.2-1.2 [153 kB] Get:106 http://ftpmaster.internal/ubuntu kinetic/main arm64 libsqlite3-0 arm64 3.39.2-1 [658 kB] Get:107 http://ftpmaster.internal/ubuntu kinetic/main arm64 openssl arm64 3.0.5-2ubuntu1 [1158 kB] Get:108 http://ftpmaster.internal/ubuntu kinetic/main arm64 libpng16-16 arm64 1.6.37-5 [185 kB] Get:109 http://ftpmaster.internal/ubuntu kinetic/main arm64 xz-utils arm64 5.2.5-2.1 [83.5 kB] Get:110 http://ftpmaster.internal/ubuntu kinetic/main arm64 advancecomp arm64 2.3-1 [167 kB] Get:111 http://ftpmaster.internal/ubuntu kinetic/main arm64 libctf0 arm64 2.39-1ubuntu1 [92.9 kB] Get:112 http://ftpmaster.internal/ubuntu kinetic/main arm64 libctf-nobfd0 arm64 2.39-1ubuntu1 [96.5 kB] Get:113 http://ftpmaster.internal/ubuntu kinetic/main arm64 libgprofng0 arm64 2.39-1ubuntu1 [791 kB] Get:114 http://ftpmaster.internal/ubuntu kinetic/main arm64 libbinutils arm64 2.39-1ubuntu1 [709 kB] Get:115 http://ftpmaster.internal/ubuntu kinetic/main arm64 binutils arm64 2.39-1ubuntu1 [3266 B] Get:116 http://ftpmaster.internal/ubuntu kinetic/main arm64 binutils-common arm64 2.39-1ubuntu1 [224 kB] Get:117 http://ftpmaster.internal/ubuntu kinetic/main arm64 binutils-aarch64-linux-gnu arm64 2.39-1ubuntu1 [3133 kB] Get:118 http://ftpmaster.internal/ubuntu kinetic/main arm64 libisl23 arm64 0.25-1 [697 kB] Get:119 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 cpp-12 arm64 12.1.0-8ubuntu2 [61.3 MB] Get:120 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 libasan8 arm64 12.1.0-8ubuntu2 [2383 kB] Get:121 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 libtsan2 arm64 12.1.0-8ubuntu2 [2513 kB] Get:122 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 libgcc-12-dev arm64 12.1.0-8ubuntu2 [1157 kB] Get:123 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 gcc-12 arm64 12.1.0-8ubuntu2 [69.5 MB] Get:124 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 libstdc++-12-dev arm64 12.1.0-8ubuntu2 [2154 kB] Get:125 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 g++-12 arm64 12.1.0-8ubuntu2 [66.3 MB] Get:126 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 g++ arm64 4:12.1.0-3ubuntu1 [1394 B] Get:127 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 gcc arm64 4:12.1.0-3ubuntu1 [5128 B] Get:128 http://ftpmaster.internal/ubuntu kinetic-proposed/main arm64 cpp arm64 4:12.1.0-3ubuntu1 [27.4 kB] Get:129 http://ftpmaster.internal/ubuntu kinetic/main arm64 g++-11 arm64 11.3.0-5ubuntu1 [11.1 MB] Get:130 http://ftpmaster.internal/ubuntu kinetic/main arm64 libstdc++-11-dev arm64 11.3.0-5ubuntu1 [2065 kB] Get:131 http://ftpmaster.internal/ubuntu kinetic/main arm64 libasan6 arm64 11.3.0-5ubuntu1 [2224 kB] Get:132 http://ftpmaster.internal/ubuntu kinetic/main arm64 gcc-11 arm64 11.3.0-5ubuntu1 [19.3 MB] Get:133 http://ftpmaster.internal/ubuntu kinetic/main arm64 libgcc-11-dev arm64 11.3.0-5ubuntu1 [1130 kB] Get:134 http://ftpmaster.internal/ubuntu kinetic/main arm64 libtsan0 arm64 11.3.0-5ubuntu1 [2240 kB] Get:135 http://ftpmaster.internal/ubuntu kinetic/main arm64 cpp-11 arm64 11.3.0-5ubuntu1 [9639 kB] Get:136 http://ftpmaster.internal/ubuntu kinetic/main arm64 gcc-11-base arm64 11.3.0-5ubuntu1 [20.4 kB] Get:137 http://ftpmaster.internal/ubuntu kinetic/main arm64 dpkg-dev all 1.21.9ubuntu1 [1070 kB] Get:138 http://ftpmaster.internal/ubuntu kinetic/main arm64 libdpkg-perl all 1.21.9ubuntu1 [237 kB] Get:139 http://ftpmaster.internal/ubuntu kinetic/main arm64 lto-disabled-list all 32 [12.2 kB] Get:140 http://ftpmaster.internal/ubuntu kinetic/main arm64 libfakeroot arm64 1.29-1ubuntu1 [30.8 kB] Get:141 http://ftpmaster.internal/ubuntu kinetic/main arm64 fakeroot arm64 1.29-1ubuntu1 [60.1 kB] Get:142 http://ftpmaster.internal/ubuntu kinetic/main arm64 libassuan0 arm64 2.5.5-4 [35.3 kB] Get:143 http://ftpmaster.internal/ubuntu kinetic/main arm64 pinentry-curses arm64 1.2.0-2ubuntu1 [33.7 kB] Get:144 http://ftpmaster.internal/ubuntu kinetic/main arm64 gpg arm64 2.2.35-3ubuntu1 [508 kB] Get:145 http://ftpmaster.internal/ubuntu kinetic/main arm64 gpgconf arm64 2.2.35-3ubuntu1 [92.4 kB] Get:146 http://ftpmaster.internal/ubuntu kinetic/main arm64 gpg-agent arm64 2.2.35-3ubuntu1 [209 kB] Get:147 http://ftpmaster.internal/ubuntu kinetic/main arm64 policyrcd-script-zg2 all 0.1-3.1 [5730 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 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Setting up g++ (4:12.1.0-3ubuntu1) ... Processing triggers for libc-bin (2.36-0ubuntu2) ... Processing triggers for debianutils (5.7-0.3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-24304739 arm64 kinetic-proposed -c chroot:build-PACKAGEBUILD-24304739 --arch=arm64 --dist=kinetic-proposed --nolog khmer_2.1.2+dfsg-11.dsc Initiating build PACKAGEBUILD-24304739 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-124-generic #140-Ubuntu SMP Thu Aug 4 02:27:01 UTC 2022 aarch64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-arm64-008.buildd +==============================================================================+ | khmer 2.1.2+dfsg-11 (arm64) Mon, 22 Aug 2022 22:01:06 +0000 | +==============================================================================+ Package: khmer Version: 2.1.2+dfsg-11 Source Version: 2.1.2+dfsg-11 Distribution: kinetic-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-24304739/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/khmer-AHvSo5/resolver-qUGCUw' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- khmer_2.1.2+dfsg-11.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/khmer-AHvSo5/khmer-2.1.2+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/khmer-AHvSo5' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, dh-exec, python3-guzzle-sphinx-theme, python3, python3-dev, python3-all-dev, python3-setuptools, python3-screed, python3-pytest, python3-pytest-runner, python3-sphinx, python3-sphinxcontrib.autoprogram, cython3, zlib1g-dev, libbz2-dev, asciidoctor, rdfind, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-python, dh-exec, python3-guzzle-sphinx-theme, python3, python3-dev, python3-all-dev, python3-setuptools, python3-screed, python3-pytest, python3-pytest-runner, python3-sphinx, python3-sphinxcontrib.autoprogram, cython3, zlib1g-dev, libbz2-dev, asciidoctor, rdfind, 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 [484 B] Get:5 copy:/<>/apt_archive ./ Packages [567 B] Fetched 2008 B in 0s (4904 B/s) Reading package lists... Reading package lists... W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 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: g++-11 libstdc++-11-dev Use 'apt autoremove' to remove them. The following additional packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bsdextrautils cython3 debhelper debugedit dh-autoreconf dh-exec dh-python dh-strip-nondeterminism docutils-common dwz file fonts-glyphicons-halflings fonts-liberation gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libdebhelper-perl libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libicu71 libjs-bootstrap libjs-jquery libjs-sphinxdoc libjs-underscore libjson-perl libmagic-mgc libmagic1 libmd0 libmpdec3 libpipeline1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libruby3.0 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 libyaml-0-2 m4 man-db media-types po-debconf python-babel-localedata python3 python3-alabaster python3-all python3-all-dev python3-attr python3-babel python3-certifi python3-chardet python3-dev python3-distutils python3-docutils python3-guzzle-sphinx-theme python3-idna python3-imagesize python3-importlib-metadata python3-iniconfig python3-jinja2 python3-lib2to3 python3-markupsafe python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pluggy python3-py python3-pygments python3-pyparsing python3-pytest python3-pytest-runner python3-requests python3-roman python3-screed python3-setuptools python3-six python3-snowballstemmer python3-sphinx python3-sphinxcontrib.autoprogram python3-tomli python3-tz python3-urllib3 python3-zipp python3.10 python3.10-dev python3.10-minimal rake rdfind ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-webrick ruby-xmlrpc ruby3.0 rubygems-integration sphinx-common xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cython-doc dh-make flit python3-build python3-installer gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python-attr-doc docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base texlive-latex-recommended python-jinja2-doc subversion python-pygments-doc ttf-bitstream-vera python-pyparsing-doc 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-sphinx-rtd-theme sphinx-doc tex-gyre texlive-fonts-recommended texlive-latex-extra texlive-plain-generic python3-brotli python3.10-venv python3.10-doc binfmt-support ri ruby-dev bundler Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl javascript-common libjson-xs-perl libltdl-dev libmail-sendmail-perl libpaper-utils python3-pil zip fonts-lato The following NEW packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bsdextrautils cython3 debhelper debugedit dh-autoreconf dh-exec dh-python dh-strip-nondeterminism docutils-common dwz file fonts-glyphicons-halflings fonts-liberation gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libdebhelper-perl libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libicu71 libjs-bootstrap libjs-jquery libjs-sphinxdoc libjs-underscore libjson-perl libmagic-mgc libmagic1 libmd0 libmpdec3 libpipeline1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libruby3.0 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 libyaml-0-2 m4 man-db media-types po-debconf python-babel-localedata python3 python3-alabaster python3-all python3-all-dev python3-attr python3-babel python3-certifi python3-chardet python3-dev python3-distutils python3-docutils python3-guzzle-sphinx-theme python3-idna python3-imagesize python3-importlib-metadata python3-iniconfig python3-jinja2 python3-lib2to3 python3-markupsafe python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pluggy python3-py python3-pygments python3-pyparsing python3-pytest python3-pytest-runner python3-requests python3-roman python3-screed python3-setuptools python3-six python3-snowballstemmer python3-sphinx python3-sphinxcontrib.autoprogram python3-tomli python3-tz python3-urllib3 python3-zipp python3.10 python3.10-dev python3.10-minimal rake rdfind ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-webrick ruby-xmlrpc ruby3.0 rubygems-integration sbuild-build-depends-main-dummy sphinx-common xml-core zlib1g-dev 0 upgraded, 120 newly installed, 0 to remove and 0 not upgraded. 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Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [780 B] Get:2 http://ftpmaster.internal/ubuntu kinetic/main arm64 libpython3.10-minimal arm64 3.10.6-1 [798 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic/main arm64 libexpat1 arm64 2.4.8-1 [77.9 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic/main arm64 python3.10-minimal arm64 3.10.6-1 [1987 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic/main arm64 python3-minimal arm64 3.10.6-1 [24.1 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main arm64 media-types all 8.0.0 [24.9 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/main arm64 libmpdec3 arm64 2.5.1-2build2 [89.0 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic/main arm64 libpython3.10-stdlib arm64 3.10.6-1 [1761 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic/main arm64 python3.10 arm64 3.10.6-1 [495 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic/main arm64 libpython3-stdlib arm64 3.10.6-1 [6848 B] Get:11 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arm64 libmagic1 arm64 1:5.41-4 [85.0 kB] Get:22 http://ftpmaster.internal/ubuntu kinetic/main arm64 file arm64 1:5.41-4 [21.6 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic/main arm64 gettext-base arm64 0.21-8 [36.8 kB] Get:24 http://ftpmaster.internal/ubuntu kinetic/main arm64 libuchardet0 arm64 0.0.7-1build2 [77.3 kB] Get:25 http://ftpmaster.internal/ubuntu kinetic/main arm64 groff-base arm64 1.22.4-8build1 [917 kB] Get:26 http://ftpmaster.internal/ubuntu kinetic/main arm64 libedit2 arm64 3.1-20210910-1build1 [96.0 kB] Get:27 http://ftpmaster.internal/ubuntu kinetic/main arm64 libpipeline1 arm64 1.5.6-2 [23.3 kB] Get:28 http://ftpmaster.internal/ubuntu kinetic/main arm64 man-db arm64 2.10.2-2 [1175 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic/main arm64 rubygems-integration all 1.18 [5336 B] Get:30 http://ftpmaster.internal/ubuntu kinetic/main arm64 rake all 13.0.6-3 [61.6 kB] Get:31 http://ftpmaster.internal/ubuntu kinetic/main arm64 ruby-net-telnet all 0.1.1-2.1 [13.1 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kinetic/main arm64 autoconf all 2.71-2 [338 kB] Get:43 http://ftpmaster.internal/ubuntu kinetic/main arm64 autotools-dev all 20220109.1 [44.9 kB] Get:44 http://ftpmaster.internal/ubuntu kinetic/main arm64 automake all 1:1.16.5-1.3 [558 kB] Get:45 http://ftpmaster.internal/ubuntu kinetic/main arm64 autopoint all 0.21-8 [421 kB] Get:46 http://ftpmaster.internal/ubuntu kinetic/universe arm64 cython3 arm64 0.29.30-1ubuntu1 [1284 kB] Get:47 http://ftpmaster.internal/ubuntu kinetic/main arm64 libdebhelper-perl all 13.9ubuntu1 [66.6 kB] Get:48 http://ftpmaster.internal/ubuntu kinetic/main arm64 libtool all 2.4.7-4 [166 kB] Get:49 http://ftpmaster.internal/ubuntu kinetic/main arm64 dh-autoreconf all 20 [16.1 kB] Get:50 http://ftpmaster.internal/ubuntu kinetic/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:51 http://ftpmaster.internal/ubuntu kinetic/main arm64 libsub-override-perl all 0.09-3 [9756 B] Get:52 http://ftpmaster.internal/ubuntu kinetic/main arm64 libfile-stripnondeterminism-perl all 1.13.0-1 [18.1 kB] Get:53 http://ftpmaster.internal/ubuntu kinetic/main arm64 dh-strip-nondeterminism all 1.13.0-1 [5344 B] Get:54 http://ftpmaster.internal/ubuntu kinetic/main arm64 libdw1 arm64 0.187-1 [241 kB] Get:55 http://ftpmaster.internal/ubuntu kinetic/main arm64 debugedit arm64 1:5.0-5 [45.9 kB] Get:56 http://ftpmaster.internal/ubuntu kinetic/main arm64 dwz arm64 0.14-1build2 [102 kB] Get:57 http://ftpmaster.internal/ubuntu kinetic/main arm64 gettext arm64 0.21-8 [842 kB] Get:58 http://ftpmaster.internal/ubuntu kinetic/main arm64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:59 http://ftpmaster.internal/ubuntu kinetic/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] Get:60 http://ftpmaster.internal/ubuntu kinetic/main arm64 debhelper all 13.9ubuntu1 [938 kB] Get:61 http://ftpmaster.internal/ubuntu kinetic/main arm64 python3-lib2to3 all 3.10.6-1 [77.5 kB] Get:62 http://ftpmaster.internal/ubuntu kinetic/main arm64 python3-distutils all 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configuration, since apt-utils is not installed Fetched 51.0 MB in 14s (3679 kB/s) Selecting previously unselected package libpython3.10-minimal:arm64. 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Setting up libpython3-stdlib:arm64 (3.10.6-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpython3.10:arm64 (3.10.6-1) ... Setting up python3.10 (3.10.6-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.10.6-1) ... Setting up man-db (2.10.2-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up python3-markupsafe (2.0.1-2build1) ... Setting up python3-tz (2022.2.1-1) ... Setting up python3-six (1.16.0-4) ... Setting up dh-autoreconf (20) ... Setting up python3-roman (3.3-1) ... Setting up python3-pyparsing (3.0.7-2) ... Setting up python3-certifi (2020.6.20-1) ... Setting up python3-snowballstemmer (2.2.0-1build1) ... Setting up sphinx-common (4.5.0-4) ... Setting up python3-idna (3.3-1) ... 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Setting up python3-all (3.10.6-1) ... Setting up debhelper (13.9ubuntu1) ... Setting up dh-exec (0.27) ... Setting up python3-zipp (1.0.0-4) ... Setting up python3-jinja2 (3.0.3-1) ... Setting up python3-pygments (2.12.0+dfsg-2) ... Setting up python3-packaging (21.3-1) ... Setting up python3-chardet (4.0.0-2) ... Setting up libpython3-all-dev:arm64 (3.10.6-1) ... Setting up python3-dev (3.10.6-1) ... Setting up python3-requests (2.27.1+dfsg-1ubuntu2) ... Setting up python3-pytest-runner (2.11.1-2) ... Setting up python3-all-dev (3.10.6-1) ... Setting up python3-importlib-metadata (4.6.4-1) ... Setting up python3-pytest (7.1.2-2ubuntu1) ... Setting up rake (13.0.6-3) ... Setting up libruby3.0:arm64 (3.0.4-7) ... Setting up ruby-rubygems (3.3.15-1) ... Setting up ruby3.0 (3.0.4-7) ... Setting up ruby (1:3.0~exp1) ... Setting up ruby-asciidoctor (2.0.16-2) ... Setting up asciidoctor (2.0.16-2) ... Processing triggers for sgml-base (1.30) ... Processing triggers for libc-bin (2.36-0ubuntu2) ... Setting up docutils-common (0.17.1+dfsg-2) ... Processing triggers for sgml-base (1.30) ... Setting up python3-docutils (0.17.1+dfsg-2) ... Setting up python3-sphinx (4.5.0-4) ... Setting up python3-guzzle-sphinx-theme (0.7.11-6) ... Setting up python3-sphinxcontrib.autoprogram (0.1.7-2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any-arm64 any-ia64 any-sparc64 all amd64) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-124-generic #140-Ubuntu SMP Thu Aug 4 02:27:01 UTC 2022 arm64 (aarch64) Toolchain package versions: binutils_2.39-1ubuntu1 dpkg-dev_1.21.9ubuntu1 g++-11_11.3.0-5ubuntu1 g++-12_12.1.0-8ubuntu2 gcc-11_11.3.0-5ubuntu1 gcc-12_12.1.0-8ubuntu2 libc6-dev_2.36-0ubuntu2 libstdc++-11-dev_11.3.0-5ubuntu1 libstdc++-12-dev_12.1.0-8ubuntu2 libstdc++6_12.1.0-8ubuntu2 linux-libc-dev_5.19.0-15.15 Package versions: adduser_3.121ubuntu1 advancecomp_2.3-1 apt_2.5.2 asciidoctor_2.0.16-2 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-8 autotools-dev_20220109.1 base-files_12.2ubuntu2 base-passwd_3.6.0 bash_5.1-6ubuntu1 binutils_2.39-1ubuntu1 binutils-aarch64-linux-gnu_2.39-1ubuntu1 binutils-common_2.39-1ubuntu1 bsdextrautils_2.38-4ubuntu1 bsdutils_1:2.38-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016 coreutils_8.32-4.1ubuntu1 cpp_4:12.1.0-3ubuntu1 cpp-11_11.3.0-5ubuntu1 cpp-12_12.1.0-8ubuntu2 cython3_0.29.30-1ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-8ubuntu1 debconf_1.5.79ubuntu1 debhelper_13.9ubuntu1 debianutils_5.7-0.3 debugedit_1:5.0-5 dh-autoreconf_20 dh-exec_0.27 dh-python_5.20220819 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 docutils-common_0.17.1+dfsg-2 dpkg_1.21.9ubuntu1 dpkg-dev_1.21.9ubuntu1 dwz_0.14-1build2 e2fsprogs_1.46.5-2ubuntu2 fakeroot_1.29-1ubuntu1 file_1:5.41-4 findutils_4.9.0-3ubuntu1 fonts-glyphicons-halflings_1.009~3.4.1+dfsg-2 fonts-liberation_1:1.07.4-11 g++_4:12.1.0-3ubuntu1 g++-11_11.3.0-5ubuntu1 g++-12_12.1.0-8ubuntu2 gcc_4:12.1.0-3ubuntu1 gcc-11_11.3.0-5ubuntu1 gcc-11-base_11.3.0-5ubuntu1 gcc-12_12.1.0-8ubuntu2 gcc-12-base_12.1.0-8ubuntu2 gettext_0.21-8 gettext-base_0.21-8 gpg_2.2.35-3ubuntu1 gpg-agent_2.2.35-3ubuntu1 gpgconf_2.2.35-3ubuntu1 gpgv_2.2.35-3ubuntu1 grep_3.7-1build1 groff-base_1.22.4-8build1 gzip_1.12-1ubuntu1 hostname_3.23ubuntu2 init_1.64 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapparmor1_3.0.7-1ubuntu1 libapt-pkg6.0_2.5.2 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libasan6_11.3.0-5ubuntu1 libasan8_12.1.0-8ubuntu2 libassuan0_2.5.5-4 libatomic1_12.1.0-8ubuntu2 libattr1_1:2.5.1-1build1 libaudit-common_1:3.0.7-1build1 libaudit1_1:3.0.7-1build1 libbinutils_2.39-1ubuntu1 libblkid1_2.38-4ubuntu1 libbsd0_0.11.6-1 libbz2-1.0_1.0.8-5build1 libbz2-dev_1.0.8-5build1 libc-bin_2.36-0ubuntu2 libc-dev-bin_2.36-0ubuntu2 libc6_2.36-0ubuntu2 libc6-dev_2.36-0ubuntu2 libcap-ng0_0.8.3-1 libcap2_1:2.44-1build3 libcc1-0_12.1.0-8ubuntu2 libcom-err2_1.46.5-2ubuntu2 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libcryptsetup12_2:2.5.0-1ubuntu1 libctf-nobfd0_2.39-1ubuntu1 libctf0_2.39-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.261ubuntu1 libdebhelper-perl_13.9ubuntu1 libdevmapper1.02.1_2:1.02.175-2.1ubuntu4 libdpkg-perl_1.21.9ubuntu1 libdw1_0.187-1 libedit2_3.1-20210910-1build1 libelf1_0.187-1 libexpat1_2.4.8-1 libexpat1-dev_2.4.8-1 libext2fs2_1.46.5-2ubuntu2 libfakeroot_1.29-1ubuntu1 libfdisk1_2.38-4ubuntu1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-11-dev_11.3.0-5ubuntu1 libgcc-12-dev_12.1.0-8ubuntu2 libgcc-s1_12.1.0-8ubuntu2 libgcrypt20_1.10.1-2ubuntu1 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgmp10_2:6.2.1+dfsg-3ubuntu1 libgnutls30_3.7.7-2ubuntu1 libgomp1_12.1.0-8ubuntu2 libgpg-error0_1.45-2 libgprofng0_2.39-1ubuntu1 libgssapi-krb5-2_1.20-1 libhogweed6_3.8.1-2 libhwasan0_12.1.0-8ubuntu2 libicu71_71.1-3 libidn2-0_2.3.3-1 libip4tc2_1.8.7-1ubuntu6 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libprocps8_2:3.3.17-7ubuntu1 libpython3-all-dev_3.10.6-1 libpython3-dev_3.10.6-1 libpython3-stdlib_3.10.6-1 libpython3.10_3.10.6-1 libpython3.10-dev_3.10.6-1 libpython3.10-minimal_3.10.6-1 libpython3.10-stdlib_3.10.6-1 libreadline8_8.1.2-1.2 libruby3.0_3.0.4-7 libseccomp2_2.5.4-1ubuntu1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol2_3.4-2 libsigsegv2_2.13-1ubuntu3 libsmartcols1_2.38-4ubuntu1 libsqlite3-0_3.39.2-1 libss2_1.46.5-2ubuntu2 libssl3_3.0.5-2ubuntu1 libstdc++-11-dev_11.3.0-5ubuntu1 libstdc++-12-dev_12.1.0-8ubuntu2 libstdc++6_12.1.0-8ubuntu2 libsub-override-perl_0.09-3 libsystemd0_251.2-2ubuntu2 libtasn1-6_4.18.0-4build1 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-4 libtsan0_11.3.0-5ubuntu1 libtsan2_12.1.0-8ubuntu2 libubsan1_12.1.0-8ubuntu2 libuchardet0_0.0.7-1build2 libudev1_251.2-2ubuntu2 libunistring2_1.0-1 libuuid1_2.38-4ubuntu1 libxml2_2.9.14+dfsg-1 libxxhash0_0.8.1-1 libyaml-0-2_0.2.5-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.0-15.15 lockfile-progs_0.1.19build1 login_1:4.11.1+dfsg1-2ubuntu1 logsave_1.46.5-2ubuntu2 lsb-base_11.2ubuntu1 lto-disabled-list_32 m4_1.4.18-5ubuntu2 make_4.3-4.1build1 man-db_2.10.2-2 mawk_1.3.4.20200120-3.1 media-types_8.0.0 mount_2.38-4ubuntu1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 openssl_3.0.5-2ubuntu1 optipng_0.7.7-2build1 passwd_1:4.11.1+dfsg1-2ubuntu1 patch_2.7.6-7build2 perl_5.34.0-5ubuntu1 perl-base_5.34.0-5ubuntu1 perl-modules-5.34_5.34.0-5ubuntu1 pinentry-curses_1.2.0-2ubuntu1 pkgbinarymangler_149 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:3.3.17-7ubuntu1 python-babel-localedata_2.8.0+dfsg.1-7 python3_3.10.6-1 python3-alabaster_0.7.12-1 python3-all_3.10.6-1 python3-all-dev_3.10.6-1 python3-attr_22.1.0-1 python3-babel_2.8.0+dfsg.1-7 python3-certifi_2020.6.20-1 python3-chardet_4.0.0-2 python3-dev_3.10.6-1 python3-distutils_3.10.6-1 python3-docutils_0.17.1+dfsg-2 python3-guzzle-sphinx-theme_0.7.11-6 python3-idna_3.3-1 python3-imagesize_1.4.1-1 python3-importlib-metadata_4.6.4-1 python3-iniconfig_1.1.1-2 python3-jinja2_3.0.3-1 python3-lib2to3_3.10.6-1 python3-markupsafe_2.0.1-2build1 python3-minimal_3.10.6-1 python3-more-itertools_8.10.0-2 python3-packaging_21.3-1 python3-pkg-resources_59.6.0-1.2 python3-pluggy_1.0.0+repack-1 python3-py_1.10.0-1 python3-pygments_2.12.0+dfsg-2 python3-pyparsing_3.0.7-2 python3-pytest_7.1.2-2ubuntu1 python3-pytest-runner_2.11.1-2 python3-requests_2.27.1+dfsg-1ubuntu2 python3-roman_3.3-1 python3-screed_1.0.5-4 python3-setuptools_59.6.0-1.2 python3-six_1.16.0-4 python3-snowballstemmer_2.2.0-1build1 python3-sphinx_4.5.0-4 python3-sphinxcontrib.autoprogram_0.1.7-2 python3-tomli_2.0.1-1 python3-tz_2022.2.1-1 python3-urllib3_1.26.9-1 python3-zipp_1.0.0-4 python3.10_3.10.6-1 python3.10-dev_3.10.6-1 python3.10-minimal_3.10.6-1 rake_13.0.6-3 rdfind_1.5.0-1.1 readline-common_8.1.2-1.2 rpcsvc-proto_1.4.2-0ubuntu6 ruby_1:3.0~exp1 ruby-asciidoctor_2.0.16-2 ruby-net-telnet_0.1.1-2.1 ruby-rubygems_3.3.15-1 ruby-webrick_1.7.0-3 ruby-xmlrpc_0.3.2-2 ruby3.0_3.0.4-7 rubygems-integration_1.18 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1ubuntu2 sensible-utils_0.0.17 sgml-base_1.30 sphinx-common_4.5.0-4 systemd_251.2-2ubuntu2 systemd-sysv_251.2-2ubuntu2 sysvinit-utils_3.01-1ubuntu1 tar_1.34+dfsg-1build3 tzdata_2022a-0ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_29ubuntu1 util-linux_2.38-4ubuntu1 util-linux-extra_2.38-4ubuntu1 xml-core_0.18+nmu1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4.1ubuntu1 zlib1g-dev_1:1.2.11.dfsg-4.1ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: khmer Binary: khmer-common, khmer, liboxli1, liboxli-dev Architecture: any-arm64 any-ia64 any-sparc64 all amd64 Version: 2.1.2+dfsg-11 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Kevin Murray Homepage: https://khmer.readthedocs.org Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/khmer Vcs-Git: https://salsa.debian.org/med-team/khmer.git Testsuite: autopkgtest Testsuite-Triggers: build-essential, libbz2-dev, pkg-config, python3-pytest, python3-pytest-runner, zlib1g-dev Build-Depends: debhelper-compat (= 13), dh-python, dh-exec, python3-guzzle-sphinx-theme, python3, python3-dev, python3-all-dev, python3-setuptools, python3-screed, python3-pytest, python3-pytest-runner, python3-sphinx, python3-sphinxcontrib.autoprogram, cython3, zlib1g-dev, libbz2-dev, asciidoctor, rdfind Package-List: khmer deb science optional arch=amd64,any-arm64,any-ia64,any-sparc64 khmer-common deb science optional arch=all liboxli-dev deb libdevel optional arch=amd64,any-arm64,any-ia64,any-sparc64 liboxli1 deb libs optional arch=amd64,any-arm64,any-ia64,any-sparc64 Checksums-Sha1: 414c7e2516edb37b8e712c12ed1075a6f081d0c7 18086617 khmer_2.1.2+dfsg.orig.tar.gz bb9bc9bada1840cfb2466dd15725cb4a1d386642 16444 khmer_2.1.2+dfsg-11.debian.tar.xz Checksums-Sha256: 7b6e01d4af574e83ccf74ea3b11b2c6ed89a4af8d01b1154d93074a0a16045c2 18086617 khmer_2.1.2+dfsg.orig.tar.gz f9648af705dbd0185ca9eecbf5953dce3d2a352acce8412053f0c628cad9861f 16444 khmer_2.1.2+dfsg-11.debian.tar.xz Files: 9cfe54c467302b3232a553494d62dbb0 18086617 khmer_2.1.2+dfsg.orig.tar.gz 42c5b0490085ca8183dd1f640c59c96c 16444 khmer_2.1.2+dfsg-11.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmMDUysACgkQPCZ2P2xn 5uJV5Q/7BTx/4w9MqDZOCgkPnIRLfoXiqVQ5Hp00zqxD9mrOikIhW+1WIuU6FzDx QoE8Ios0Tp+h89L9Mz/0ts0xpQNhR9men26o+WbDxZ4tzWMV0XJy+k11pySP2pEd E3c2HpyEU/ffE0o0BhN7niQJXJKcZm5f4syqFgpZbayuBnomG2f9Ruq4OM2/8I8E pliSUUlAKc93jFHONB50zl4XOLlVB+6Wr9rdvMaqf7d/BeJwINA+9WMNbL+EvZqm J6UgAvNbpN5DFrrc5W9q5fPLACXG/fS76o2WcyWzaaT/DTvPap+m2QYnQR6fMUQG lpZlAivC/5YsfY7wbMDf0f23xsKc3JnVN6GZsVyJ5t/gl9o/8gvc00hszLqi2t74 a3lhRzXOUdRDbhya137HqCLQIghuPrberJk02TD0ql7szN8cISwJg+8j5ftJh2o1 +WnYoDW1jxr7hlDVAPVWTWt4Y1kj1pd7IZVv/vdKHUX4/ueYNWogS4E7rXvjDNot 1r69xzH87Mdlxdkt/oXSx9tIgsWduSQ5VC2tgwER/L1jJ5VuBBVfxMU9OxJCeGGH 1d+4U8tHg4qfHf9uT3JFSfdv1d2yzRQiXU4Ib2PqOV63mqcbTXuS0YdY3mS9O9we nI7dFjB4iQtjqxzq/+4B2HPU1pBViP/cPBJhYQz+s1lGjkTc9PM= =tnEX -----END PGP SIGNATURE----- gpgv: Signature made Mon Aug 22 09:58:03 2022 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./khmer_2.1.2+dfsg-11.dsc dpkg-source: info: extracting khmer in /<> dpkg-source: info: unpacking khmer_2.1.2+dfsg.orig.tar.gz dpkg-source: info: unpacking khmer_2.1.2+dfsg-11.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying update-manifest dpkg-source: info: applying setup-py-py3 dpkg-source: info: applying local-libs dpkg-source: info: applying older-setuptools dpkg-source: info: applying disable_google_analytics dpkg-source: info: applying get_version dpkg-source: info: applying install-prefix dpkg-source: info: applying cpython-bug-empty-exceptions dpkg-source: info: applying amend-skip dpkg-source: info: applying setup.py-py3 dpkg-source: info: applying python3 dpkg-source: info: applying fix_liboxli_test dpkg-source: info: applying gcc11.patch dpkg-source: info: applying bz2.patch dpkg-source: info: applying stringio-buffer.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-24304739 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-24304739 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-24304739 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 khmer dpkg-buildpackage: info: source version 2.1.2+dfsg-11 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean || /bin/true install -d /<>/khmer-2.1.2\+dfsg/debian/.debhelper/generated/_source/home pybuild --clean -i python{version} -p 3.10 I: pybuild base:240: python3.10 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead warnings.warn( running clean removing '/<>/.pybuild/cpython3_3.10_khmer/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.10' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; cd src/oxli && /usr/bin/make clean make[2]: Entering directory '/<>/src/oxli' rm -f *.o *.a *.so* oxli.pc make[2]: Leaving directory '/<>/src/oxli' rm -rf __pycache__ .eggs make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/khmer-common.substvars debian/khmer.substvars debian/liboxli1.substvars debian/liboxli-dev.substvars debian/files rm -fr -- debian/khmer-common/ debian/tmp/ debian/khmer/ debian/liboxli1/ debian/liboxli-dev/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary-arch dh binary-arch --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild install -d /<>/khmer-2.1.2\+dfsg/debian/.debhelper/generated/_source/home pybuild --configure -i python{version} -p 3.10 I: pybuild base:240: python3.10 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead warnings.warn( running config debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build pybuild --build -i python{version} -p 3.10 I: pybuild base:240: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead warnings.warn( running build running build_py creating /<>/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/trimming.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/khmer_args.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/kfile.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/khmer_logger.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/_version.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/__init__.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/utils.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/thread_utils.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer creating /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_cython_parsing.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_banding.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_script_arguments.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_labelhash.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_cython_assembly.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_functions.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_lump.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/graph_features.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_nibblestorage.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_hashset.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_sandbox_scripts.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_nodegraph.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_version.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_read_aligner.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_countgraph.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_read_handling.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_threaded_sequence_processor.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_hll.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_counttable.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_normalize_by_median.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_scripts.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_subset_graph.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/__init__.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/khmer_tst_utils.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_cpython_hierarchy.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_sequence_validation.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_filter_abund.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_counting_single.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_script_output.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_read_parsers.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_tabletype.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_oxli_functions.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_streaming_io.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_graph.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests creating /<>/.pybuild/cpython3_3.10_khmer/build/oxli copying oxli/build_graph.py -> /<>/.pybuild/cpython3_3.10_khmer/build/oxli copying oxli/functions.py -> /<>/.pybuild/cpython3_3.10_khmer/build/oxli copying oxli/__init__.py -> /<>/.pybuild/cpython3_3.10_khmer/build/oxli copying oxli/partition.py -> /<>/.pybuild/cpython3_3.10_khmer/build/oxli creating /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/__init__.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli running egg_info creating khmer.egg-info writing khmer.egg-info/PKG-INFO writing dependency_links to khmer.egg-info/dependency_links.txt writing requirements to khmer.egg-info/requires.txt writing top-level names to khmer.egg-info/top_level.txt writing manifest file 'khmer.egg-info/SOURCES.txt' reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.hh' under directory 'khmer' warning: no files found matching '*.cpp' under directory 'khmer/_oxli' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching '*.c' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '[Mm]akefile*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'khmer.egg-info/SOURCES.txt' copying tests/.gitignore -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests creating /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.bz2 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.gz -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.truncated.bz2 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.truncated.gz -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/README.rst -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/all-A.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k12.ct -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k12.ht -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k32.stoptags -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k32.tagset -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/banding-reads.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/biglump-random-20-a.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/bogus.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/casava_18-pe.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/combine_parts_1.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-all-paired-all-keep.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-none-paired.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-some-paired-all-keep.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file.bz2 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file.gz -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/fakelump.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/fakelump.fa.stoptags.txt -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/filter-test-A.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/filter-test-B.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k12.ht -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k12.ht.gz -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k32.stoptags -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k32.tagset -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/multi-output.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/normC20k20.ct -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/old-style-format-w-comments.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.1 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.2 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.badleft -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.badright -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.paired_bad -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken2.fq.1 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken2.fq.2 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken3.fq.1 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken3.fq.2 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken4.fq.1 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken4.fq.2 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-2.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-broken.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-witherror.fa.pe -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa.pe -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa.se -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq.pe -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq.se -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq.1 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq.2 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa.1 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa.2 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq.1 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq.2 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired.malformat.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired.malformat.fq.2 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired_one.base.dif.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-X2.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.even.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.bz2 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.gz -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.part -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq.bz2 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq.gz -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.odd.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-b.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-31-c.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/readaligner-default.json -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/readaligner-k12.json -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/real-partition-small.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/real-partition-tiny.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/simple-genome-reads.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/simple-genome.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/single-read.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/single-read.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa.bz2 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa.gz -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.paired.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.paired2.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-3.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-impaired.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-paired.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-paired.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-empty.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-empty.fa.bz2 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-error-reads.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-n-reads.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-reads.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-reads.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-filter-abund-Ns.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph2.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph5.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-labels.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-large.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-multi.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-output-partitions.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-overlap1.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-overlap2.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fq.bz2 -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fq.gz -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-short.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-contigs.fp -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-reads.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-reads.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-transcript.fa -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/truncated.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/unclean-reads.fastq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/valid-read-testing.fq -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying khmer/_oxli/assembly.pxd -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/assembly.pyx -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.pxd -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.pyx -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.pxd -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.pyx -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/hllcounter.pxd -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/oxli_types.pxd -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.pxd -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.pyx -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/traversal.pxd -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/utils.pxd -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/utils.pyx -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli UPDATING /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_version.py set /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_version.py to '2.1.2' running build_ext cythoning khmer/_oxli/assembly.pyx to khmer/_oxli/assembly.cpp /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/khmer/_oxli/assembly.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: khmer/_oxli/parsing.pxd:159:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:161:34: Declarations should not be declared inline. cythoning khmer/_oxli/parsing.pyx to khmer/_oxli/parsing.cpp /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/khmer/_oxli/parsing.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: khmer/_oxli/parsing.pxd:159:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:161:34: Declarations should not be declared inline. cythoning khmer/_oxli/hashing.pyx to khmer/_oxli/hashing.cpp /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/khmer/_oxli/hashing.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning khmer/_oxli/graphs.pyx to khmer/_oxli/graphs.cpp /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/khmer/_oxli/graphs.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: khmer/_oxli/parsing.pxd:159:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:161:34: Declarations should not be declared inline. cythoning khmer/_oxli/utils.pyx to khmer/_oxli/utils.cpp /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/khmer/_oxli/utils.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'khmer._khmer' extension creating build creating build/temp.linux-arm64-3.10 creating build/temp.linux-arm64-3.10/src creating build/temp.linux-arm64-3.10/src/khmer creating build/temp.linux-arm64-3.10/src/oxli creating build/temp.linux-arm64-3.10/third-party creating build/temp.linux-arm64-3.10/third-party/smhasher aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_countgraph.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_counttable.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_graphlabels.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashgraph.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashset.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashtable.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hllcounter.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_nodegraph.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_nodetable.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_readaligner.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_smallcountgraph.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_smallcounttable.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_subsetpartition.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_utils.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/alphabets.cc -o build/temp.linux-arm64-3.10/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/assembler.cc -o build/temp.linux-arm64-3.10/src/oxli/assembler.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor ‘oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)’: include/oxli/assembler.hh:80:23: warning: ‘oxli::LinearAssembler::graph’ will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ include/oxli/assembler.hh:79:16: warning: ‘oxli::WordLength oxli::LinearAssembler::_ksize’ [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor ‘oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()’: src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type ‘oxli::LinearAssembler’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh: In constructor ‘oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)’: include/oxli/assembler.hh:158:16: warning: ‘oxli::JunctionCountAssembler::_ksize’ will be initialized after [-Wreorder] 158 | WordLength _ksize; | ^~~~~~ include/oxli/assembler.hh:153:15: warning: ‘oxli::Traverser oxli::JunctionCountAssembler::traverser’ [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh:153:15: warning: ‘oxli::JunctionCountAssembler::traverser’ will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ include/oxli/assembler.hh:151:21: warning: ‘oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm’ [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hashgraph.cc -o build/temp.linux-arm64-3.10/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hashtable.cc -o build/temp.linux-arm64-3.10/src/oxli/hashtable.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hashtable.cc:512:1: required from here src/oxli/hashtable.cc:103:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 103 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hashtable.cc:529:1: required from here src/oxli/hashtable.cc:133:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 133 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hllcounter.cc -o build/temp.linux-arm64-3.10/src/oxli/hllcounter.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hllcounter.cc: In instantiation of ‘void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hllcounter.cc:524:1: required from here src/oxli/hllcounter.cc:428:40: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 428 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/kmer_filters.cc -o build/temp.linux-arm64-3.10/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/kmer_hash.cc -o build/temp.linux-arm64-3.10/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/labelhash.cc -o build/temp.linux-arm64-3.10/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/read_aligner.cc -o build/temp.linux-arm64-3.10/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/read_parsers.cc -o build/temp.linux-arm64-3.10/src/oxli/read_parsers.o -O3 -std=c++11 -pedantic -fopenmp In file included from third-party/seqan/core/include/seqan/basic.h:62, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/modifier.h:66, from third-party/seqan/core/include/seqan/file.h:48, from third-party/seqan/core/include/seqan/stream.h:70, from third-party/seqan/core/include/seqan/seq_io.h:45: third-party/seqan/core/include/seqan/modifier/modifier_functors.h:68:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 68 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from src/oxli/read_parsers.cc:38: /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:91:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 91 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:169:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 169 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:178:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 178 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:188:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 188 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:198:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 198 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:208:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 208 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:217:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 217 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:229:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/file.h:117: third-party/seqan/core/include/seqan/file/string_external.h:1316:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1316 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/graph_algorithms.h:46, from third-party/seqan/core/include/seqan/graph_align.h:47, from third-party/seqan/core/include/seqan/align.h:54, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83: third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:340:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 340 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/graph_algorithms.h:47: third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm.h:643:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 643 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:79: third-party/seqan/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:116: third-party/seqan/core/include/seqan/align/dp_cell_affine.h: In member function ‘seqan::DPCell_ >& seqan::DPCell_ >::operator=(const seqan::DPCell_ >&)’: third-party/seqan/core/include/seqan/align/dp_cell_affine.h:84:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 84 | if (this != &other) | ^~ third-party/seqan/core/include/seqan/align/dp_cell_affine.h:86:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 86 | _horizontalScore = other._horizontalScore; | ^~~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:166: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from third-party/seqan/core/include/seqan/align.h:174: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41: third-party/seqan/core/include/seqan/bam_io/bam_stream.h: At global scope: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:59: third-party/seqan/core/include/seqan/store/store_align.h:322:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 322 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:332:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 332 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:342:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:352:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:362:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:372:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61: third-party/seqan/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1733 | if (alignQualityStoreLengthPre == 0u) | ^~ third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/storage.cc -o build/temp.linux-arm64-3.10/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/subset.cc -o build/temp.linux-arm64-3.10/src/oxli/subset.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/subset.cc: In member function ‘size_t oxli::SubsetPartition::output_partitioned_file(const std::string&, const std::string&, bool, oxli::CallbackFn, void*)’: src/oxli/subset.cc:136:24: warning: unused variable ‘ksize’ [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/traversal.cc -o build/temp.linux-arm64-3.10/src/oxli/traversal.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:202:5: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:203:5: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-arm64-3.10/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-arm64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-arm64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-arm64-3.10/src/khmer/_cpy_utils.o build/temp.linux-arm64-3.10/src/oxli/alphabets.o build/temp.linux-arm64-3.10/src/oxli/assembler.o build/temp.linux-arm64-3.10/src/oxli/hashgraph.o build/temp.linux-arm64-3.10/src/oxli/hashtable.o build/temp.linux-arm64-3.10/src/oxli/hllcounter.o build/temp.linux-arm64-3.10/src/oxli/kmer_filters.o build/temp.linux-arm64-3.10/src/oxli/kmer_hash.o build/temp.linux-arm64-3.10/src/oxli/labelhash.o build/temp.linux-arm64-3.10/src/oxli/read_aligner.o build/temp.linux-arm64-3.10/src/oxli/read_parsers.o build/temp.linux-arm64-3.10/src/oxli/storage.o build/temp.linux-arm64-3.10/src/oxli/subset.o build/temp.linux-arm64-3.10/src/oxli/traversal.o build/temp.linux-arm64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_khmer.cpython-310-aarch64-linux-gnu.so -fopenmp building 'khmer._oxli.assembly' extension creating build/temp.linux-arm64-3.10/khmer creating build/temp.linux-arm64-3.10/khmer/_oxli aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c khmer/_oxli/assembly.cpp -o build/temp.linux-arm64-3.10/khmer/_oxli/assembly.o -O3 -std=c++11 -pedantic -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:740: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/assembly.cpp:620: note: this is the location of the previous definition 620 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/assembly.cpp:627: note: this is the location of the previous definition 627 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/assembly.cpp:624: note: this is the location of the previous definition 624 | #define PyInt_FromLong PyLong_FromLong | aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.10/khmer/_oxli/assembly.o build/temp.linux-arm64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-arm64-3.10/src/khmer/_cpy_utils.o build/temp.linux-arm64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-arm64-3.10/src/oxli/read_parsers.o build/temp.linux-arm64-3.10/src/oxli/kmer_hash.o build/temp.linux-arm64-3.10/src/oxli/hashtable.o build/temp.linux-arm64-3.10/src/oxli/hashgraph.o build/temp.linux-arm64-3.10/src/oxli/labelhash.o build/temp.linux-arm64-3.10/src/oxli/subset.o build/temp.linux-arm64-3.10/src/oxli/read_aligner.o build/temp.linux-arm64-3.10/src/oxli/hllcounter.o build/temp.linux-arm64-3.10/src/oxli/traversal.o build/temp.linux-arm64-3.10/src/oxli/kmer_filters.o build/temp.linux-arm64-3.10/src/oxli/assembler.o build/temp.linux-arm64-3.10/src/oxli/alphabets.o build/temp.linux-arm64-3.10/src/oxli/storage.o build/temp.linux-arm64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.cpython-310-aarch64-linux-gnu.so -fopenmp building 'khmer._oxli.parsing' extension aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c khmer/_oxli/parsing.cpp -o build/temp.linux-arm64-3.10/khmer/_oxli/parsing.o -O3 -std=c++11 -pedantic -fopenmp khmer/_oxli/parsing.cpp: In function ‘bool __pyx_f_5khmer_5_oxli_7parsing_sanitize_sequence(std::string&, std::string&, bool)’: khmer/_oxli/parsing.cpp:5846:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 5846 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { | ~~~~~~~~~~^~~~~~~~~~~ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.10/khmer/_oxli/parsing.o build/temp.linux-arm64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-arm64-3.10/src/khmer/_cpy_utils.o build/temp.linux-arm64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-arm64-3.10/src/oxli/read_parsers.o build/temp.linux-arm64-3.10/src/oxli/kmer_hash.o build/temp.linux-arm64-3.10/src/oxli/hashtable.o build/temp.linux-arm64-3.10/src/oxli/hashgraph.o build/temp.linux-arm64-3.10/src/oxli/labelhash.o build/temp.linux-arm64-3.10/src/oxli/subset.o build/temp.linux-arm64-3.10/src/oxli/read_aligner.o build/temp.linux-arm64-3.10/src/oxli/hllcounter.o build/temp.linux-arm64-3.10/src/oxli/traversal.o build/temp.linux-arm64-3.10/src/oxli/kmer_filters.o build/temp.linux-arm64-3.10/src/oxli/assembler.o build/temp.linux-arm64-3.10/src/oxli/alphabets.o build/temp.linux-arm64-3.10/src/oxli/storage.o build/temp.linux-arm64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/parsing.cpython-310-aarch64-linux-gnu.so -fopenmp building 'khmer._oxli.hashing' extension aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c khmer/_oxli/hashing.cpp -o build/temp.linux-arm64-3.10/khmer/_oxli/hashing.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.10/khmer/_oxli/hashing.o build/temp.linux-arm64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-arm64-3.10/src/khmer/_cpy_utils.o build/temp.linux-arm64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-arm64-3.10/src/oxli/read_parsers.o build/temp.linux-arm64-3.10/src/oxli/kmer_hash.o build/temp.linux-arm64-3.10/src/oxli/hashtable.o build/temp.linux-arm64-3.10/src/oxli/hashgraph.o build/temp.linux-arm64-3.10/src/oxli/labelhash.o build/temp.linux-arm64-3.10/src/oxli/subset.o build/temp.linux-arm64-3.10/src/oxli/read_aligner.o build/temp.linux-arm64-3.10/src/oxli/hllcounter.o build/temp.linux-arm64-3.10/src/oxli/traversal.o build/temp.linux-arm64-3.10/src/oxli/kmer_filters.o build/temp.linux-arm64-3.10/src/oxli/assembler.o build/temp.linux-arm64-3.10/src/oxli/alphabets.o build/temp.linux-arm64-3.10/src/oxli/storage.o build/temp.linux-arm64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.cpython-310-aarch64-linux-gnu.so -fopenmp building 'khmer._oxli.graphs' extension aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c khmer/_oxli/graphs.cpp -o build/temp.linux-arm64-3.10/khmer/_oxli/graphs.o -O3 -std=c++11 -pedantic -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:740: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/graphs.cpp:620: note: this is the location of the previous definition 620 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/graphs.cpp:627: note: this is the location of the previous definition 627 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/graphs.cpp:624: note: this is the location of the previous definition 624 | #define PyInt_FromLong PyLong_FromLong | aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.10/khmer/_oxli/graphs.o build/temp.linux-arm64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-arm64-3.10/src/khmer/_cpy_utils.o build/temp.linux-arm64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-arm64-3.10/src/oxli/read_parsers.o build/temp.linux-arm64-3.10/src/oxli/kmer_hash.o build/temp.linux-arm64-3.10/src/oxli/hashtable.o build/temp.linux-arm64-3.10/src/oxli/hashgraph.o build/temp.linux-arm64-3.10/src/oxli/labelhash.o build/temp.linux-arm64-3.10/src/oxli/subset.o build/temp.linux-arm64-3.10/src/oxli/read_aligner.o build/temp.linux-arm64-3.10/src/oxli/hllcounter.o build/temp.linux-arm64-3.10/src/oxli/traversal.o build/temp.linux-arm64-3.10/src/oxli/kmer_filters.o build/temp.linux-arm64-3.10/src/oxli/assembler.o build/temp.linux-arm64-3.10/src/oxli/alphabets.o build/temp.linux-arm64-3.10/src/oxli/storage.o build/temp.linux-arm64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/graphs.cpython-310-aarch64-linux-gnu.so -fopenmp building 'khmer._oxli.utils' extension aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c khmer/_oxli/utils.cpp -o build/temp.linux-arm64-3.10/khmer/_oxli/utils.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.10/khmer/_oxli/utils.o build/temp.linux-arm64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-arm64-3.10/src/khmer/_cpy_utils.o build/temp.linux-arm64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-arm64-3.10/src/oxli/read_parsers.o build/temp.linux-arm64-3.10/src/oxli/kmer_hash.o build/temp.linux-arm64-3.10/src/oxli/hashtable.o build/temp.linux-arm64-3.10/src/oxli/hashgraph.o build/temp.linux-arm64-3.10/src/oxli/labelhash.o build/temp.linux-arm64-3.10/src/oxli/subset.o build/temp.linux-arm64-3.10/src/oxli/read_aligner.o build/temp.linux-arm64-3.10/src/oxli/hllcounter.o build/temp.linux-arm64-3.10/src/oxli/traversal.o build/temp.linux-arm64-3.10/src/oxli/kmer_filters.o build/temp.linux-arm64-3.10/src/oxli/assembler.o build/temp.linux-arm64-3.10/src/oxli/alphabets.o build/temp.linux-arm64-3.10/src/oxli/storage.o build/temp.linux-arm64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/utils.cpython-310-aarch64-linux-gnu.so -fopenmp running build_scripts creating build/scripts-3.10 copying and adjusting scripts/annotate-partitions.py -> build/scripts-3.10 copying and adjusting scripts/find-knots.py -> build/scripts-3.10 copying and adjusting scripts/load-into-counting.py -> build/scripts-3.10 copying and adjusting scripts/partition-graph.py -> build/scripts-3.10 copying and adjusting scripts/trim-low-abund.py -> build/scripts-3.10 copying and adjusting scripts/filter-stoptags.py -> build/scripts-3.10 copying and adjusting scripts/extract-long-sequences.py -> build/scripts-3.10 copying and adjusting scripts/normalize-by-median.py -> build/scripts-3.10 copying and adjusting scripts/readstats.py -> build/scripts-3.10 copying and adjusting scripts/make-initial-stoptags.py -> build/scripts-3.10 copying and adjusting scripts/unique-kmers.py -> build/scripts-3.10 copying and adjusting scripts/merge-partitions.py -> build/scripts-3.10 copying and adjusting scripts/filter-abund.py -> build/scripts-3.10 copying and adjusting scripts/load-graph.py -> build/scripts-3.10 copying and adjusting scripts/abundance-dist-single.py -> build/scripts-3.10 copying and adjusting scripts/extract-paired-reads.py -> build/scripts-3.10 copying and adjusting scripts/interleave-reads.py -> build/scripts-3.10 copying and adjusting scripts/do-partition.py -> build/scripts-3.10 copying and adjusting scripts/sample-reads-randomly.py -> build/scripts-3.10 copying and adjusting scripts/abundance-dist.py -> build/scripts-3.10 copying and adjusting scripts/extract-partitions.py -> build/scripts-3.10 copying and adjusting scripts/fastq-to-fasta.py -> build/scripts-3.10 copying and adjusting scripts/split-paired-reads.py -> build/scripts-3.10 copying and adjusting scripts/count-median.py -> build/scripts-3.10 copying and adjusting scripts/filter-abund-single.py -> build/scripts-3.10 changing mode of build/scripts-3.10/annotate-partitions.py from 644 to 755 changing mode of build/scripts-3.10/find-knots.py from 644 to 755 changing mode of build/scripts-3.10/load-into-counting.py from 644 to 755 changing mode of build/scripts-3.10/partition-graph.py from 644 to 755 changing mode of build/scripts-3.10/trim-low-abund.py from 644 to 755 changing mode of build/scripts-3.10/filter-stoptags.py from 644 to 755 changing mode of build/scripts-3.10/extract-long-sequences.py from 644 to 755 changing mode of build/scripts-3.10/normalize-by-median.py from 644 to 755 changing mode of build/scripts-3.10/readstats.py from 644 to 755 changing mode of build/scripts-3.10/make-initial-stoptags.py from 644 to 755 changing mode of build/scripts-3.10/unique-kmers.py from 644 to 755 changing mode of build/scripts-3.10/merge-partitions.py from 644 to 755 changing mode of build/scripts-3.10/filter-abund.py from 644 to 755 changing mode of build/scripts-3.10/load-graph.py from 644 to 755 changing mode of build/scripts-3.10/abundance-dist-single.py from 644 to 755 changing mode of build/scripts-3.10/extract-paired-reads.py from 644 to 755 changing mode of build/scripts-3.10/interleave-reads.py from 644 to 755 changing mode of build/scripts-3.10/do-partition.py from 644 to 755 changing mode of build/scripts-3.10/sample-reads-randomly.py from 644 to 755 changing mode of build/scripts-3.10/abundance-dist.py from 644 to 755 changing mode of build/scripts-3.10/extract-partitions.py from 644 to 755 changing mode of build/scripts-3.10/fastq-to-fasta.py from 644 to 755 changing mode of build/scripts-3.10/split-paired-reads.py from 644 to 755 changing mode of build/scripts-3.10/count-median.py from 644 to 755 changing mode of build/scripts-3.10/filter-abund-single.py from 644 to 755 ln -sf "`pwd`"/.pybuild/pythonX.Y_*/build/khmer/*.so khmer && \ ./setup.py develop --user && ./setup.py build_sphinx /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead warnings.warn( running develop /usr/lib/python3/dist-packages/setuptools/command/easy_install.py:158: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools. warnings.warn( /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running egg_info writing khmer.egg-info/PKG-INFO writing dependency_links to khmer.egg-info/dependency_links.txt writing requirements to khmer.egg-info/requires.txt writing top-level names to khmer.egg-info/top_level.txt reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.hh' under directory 'khmer' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching '*.c' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '[Mm]akefile*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'khmer.egg-info/SOURCES.txt' running build_ext skipping 'khmer/_oxli/assembly.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/parsing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/hashing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/graphs.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/utils.cpp' Cython extension (up-to-date) building 'khmer._khmer' extension creating build/temp.linux-aarch64-3.10 creating build/temp.linux-aarch64-3.10/src creating build/temp.linux-aarch64-3.10/src/khmer creating build/temp.linux-aarch64-3.10/src/oxli creating build/temp.linux-aarch64-3.10/third-party creating build/temp.linux-aarch64-3.10/third-party/smhasher aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_countgraph.cc -o build/temp.linux-aarch64-3.10/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_counttable.cc -o build/temp.linux-aarch64-3.10/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_graphlabels.cc -o build/temp.linux-aarch64-3.10/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashgraph.cc -o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashset.cc -o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashtable.cc -o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hllcounter.cc -o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-aarch64-3.10/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_nodegraph.cc -o build/temp.linux-aarch64-3.10/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_nodetable.cc -o build/temp.linux-aarch64-3.10/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_readaligner.cc -o build/temp.linux-aarch64-3.10/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-aarch64-3.10/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_smallcountgraph.cc -o build/temp.linux-aarch64-3.10/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_smallcounttable.cc -o build/temp.linux-aarch64-3.10/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_subsetpartition.cc -o build/temp.linux-aarch64-3.10/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_utils.cc -o build/temp.linux-aarch64-3.10/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/alphabets.cc -o build/temp.linux-aarch64-3.10/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/assembler.cc -o build/temp.linux-aarch64-3.10/src/oxli/assembler.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor ‘oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)’: include/oxli/assembler.hh:80:23: warning: ‘oxli::LinearAssembler::graph’ will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ include/oxli/assembler.hh:79:16: warning: ‘oxli::WordLength oxli::LinearAssembler::_ksize’ [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor ‘oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()’: src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type ‘oxli::LinearAssembler’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh: In constructor ‘oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)’: include/oxli/assembler.hh:158:16: warning: ‘oxli::JunctionCountAssembler::_ksize’ will be initialized after [-Wreorder] 158 | WordLength _ksize; | ^~~~~~ include/oxli/assembler.hh:153:15: warning: ‘oxli::Traverser oxli::JunctionCountAssembler::traverser’ [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh:153:15: warning: ‘oxli::JunctionCountAssembler::traverser’ will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ include/oxli/assembler.hh:151:21: warning: ‘oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm’ [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hashgraph.cc -o build/temp.linux-aarch64-3.10/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hashtable.cc -o build/temp.linux-aarch64-3.10/src/oxli/hashtable.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hashtable.cc:512:1: required from here src/oxli/hashtable.cc:103:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 103 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hashtable.cc:529:1: required from here src/oxli/hashtable.cc:133:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 133 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hllcounter.cc -o build/temp.linux-aarch64-3.10/src/oxli/hllcounter.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hllcounter.cc: In instantiation of ‘void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hllcounter.cc:524:1: required from here src/oxli/hllcounter.cc:428:40: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 428 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/kmer_filters.cc -o build/temp.linux-aarch64-3.10/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/kmer_hash.cc -o build/temp.linux-aarch64-3.10/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/labelhash.cc -o build/temp.linux-aarch64-3.10/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/read_aligner.cc -o build/temp.linux-aarch64-3.10/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/read_parsers.cc -o build/temp.linux-aarch64-3.10/src/oxli/read_parsers.o -O3 -std=c++11 -pedantic -fopenmp In file included from third-party/seqan/core/include/seqan/basic.h:62, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/modifier.h:66, from third-party/seqan/core/include/seqan/file.h:48, from third-party/seqan/core/include/seqan/stream.h:70, from third-party/seqan/core/include/seqan/seq_io.h:45: third-party/seqan/core/include/seqan/modifier/modifier_functors.h:68:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 68 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from src/oxli/read_parsers.cc:38: /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:91:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 91 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:169:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 169 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:178:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 178 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:188:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 188 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:198:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 198 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:208:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 208 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:217:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 217 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:229:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/file.h:117: third-party/seqan/core/include/seqan/file/string_external.h:1316:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1316 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/graph_algorithms.h:46, from third-party/seqan/core/include/seqan/graph_align.h:47, from third-party/seqan/core/include/seqan/align.h:54, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83: third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:340:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 340 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/graph_algorithms.h:47: third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm.h:643:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 643 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:79: third-party/seqan/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:116: third-party/seqan/core/include/seqan/align/dp_cell_affine.h: In member function ‘seqan::DPCell_ >& seqan::DPCell_ >::operator=(const seqan::DPCell_ >&)’: third-party/seqan/core/include/seqan/align/dp_cell_affine.h:84:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 84 | if (this != &other) | ^~ third-party/seqan/core/include/seqan/align/dp_cell_affine.h:86:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 86 | _horizontalScore = other._horizontalScore; | ^~~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:166: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from third-party/seqan/core/include/seqan/align.h:174: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41: third-party/seqan/core/include/seqan/bam_io/bam_stream.h: At global scope: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:59: third-party/seqan/core/include/seqan/store/store_align.h:322:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 322 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:332:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 332 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:342:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:352:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:362:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:372:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61: third-party/seqan/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1733 | if (alignQualityStoreLengthPre == 0u) | ^~ third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/storage.cc -o build/temp.linux-aarch64-3.10/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/subset.cc -o build/temp.linux-aarch64-3.10/src/oxli/subset.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/subset.cc: In member function ‘size_t oxli::SubsetPartition::output_partitioned_file(const std::string&, const std::string&, bool, oxli::CallbackFn, void*)’: src/oxli/subset.cc:136:24: warning: unused variable ‘ksize’ [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/traversal.cc -o build/temp.linux-aarch64-3.10/src/oxli/traversal.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:202:5: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:203:5: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-aarch64-3.10/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp creating build/lib.linux-aarch64-3.10 creating build/lib.linux-aarch64-3.10/khmer aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_utils.o build/temp.linux-aarch64-3.10/src/oxli/alphabets.o build/temp.linux-aarch64-3.10/src/oxli/assembler.o build/temp.linux-aarch64-3.10/src/oxli/hashgraph.o build/temp.linux-aarch64-3.10/src/oxli/hashtable.o build/temp.linux-aarch64-3.10/src/oxli/hllcounter.o build/temp.linux-aarch64-3.10/src/oxli/kmer_filters.o build/temp.linux-aarch64-3.10/src/oxli/kmer_hash.o build/temp.linux-aarch64-3.10/src/oxli/labelhash.o build/temp.linux-aarch64-3.10/src/oxli/read_aligner.o build/temp.linux-aarch64-3.10/src/oxli/read_parsers.o build/temp.linux-aarch64-3.10/src/oxli/storage.o build/temp.linux-aarch64-3.10/src/oxli/subset.o build/temp.linux-aarch64-3.10/src/oxli/traversal.o build/temp.linux-aarch64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-aarch64-3.10/khmer/_khmer.cpython-310-aarch64-linux-gnu.so -fopenmp building 'khmer._oxli.assembly' extension creating build/temp.linux-aarch64-3.10/khmer creating build/temp.linux-aarch64-3.10/khmer/_oxli aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c khmer/_oxli/assembly.cpp -o build/temp.linux-aarch64-3.10/khmer/_oxli/assembly.o -O3 -std=c++11 -pedantic -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:740: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/assembly.cpp:620: note: this is the location of the previous definition 620 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/assembly.cpp:627: note: this is the location of the previous definition 627 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/assembly.cpp:624: note: this is the location of the previous definition 624 | #define PyInt_FromLong PyLong_FromLong | creating build/lib.linux-aarch64-3.10/khmer/_oxli aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.10/khmer/_oxli/assembly.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_utils.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-aarch64-3.10/src/oxli/read_parsers.o build/temp.linux-aarch64-3.10/src/oxli/kmer_hash.o build/temp.linux-aarch64-3.10/src/oxli/hashtable.o build/temp.linux-aarch64-3.10/src/oxli/hashgraph.o build/temp.linux-aarch64-3.10/src/oxli/labelhash.o build/temp.linux-aarch64-3.10/src/oxli/subset.o build/temp.linux-aarch64-3.10/src/oxli/read_aligner.o build/temp.linux-aarch64-3.10/src/oxli/hllcounter.o build/temp.linux-aarch64-3.10/src/oxli/traversal.o build/temp.linux-aarch64-3.10/src/oxli/kmer_filters.o build/temp.linux-aarch64-3.10/src/oxli/assembler.o build/temp.linux-aarch64-3.10/src/oxli/alphabets.o build/temp.linux-aarch64-3.10/src/oxli/storage.o build/temp.linux-aarch64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-aarch64-3.10/khmer/_oxli/assembly.cpython-310-aarch64-linux-gnu.so -fopenmp building 'khmer._oxli.parsing' extension aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c khmer/_oxli/parsing.cpp -o build/temp.linux-aarch64-3.10/khmer/_oxli/parsing.o -O3 -std=c++11 -pedantic -fopenmp khmer/_oxli/parsing.cpp: In function ‘bool __pyx_f_5khmer_5_oxli_7parsing_sanitize_sequence(std::string&, std::string&, bool)’: khmer/_oxli/parsing.cpp:5846:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 5846 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { | ~~~~~~~~~~^~~~~~~~~~~ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.10/khmer/_oxli/parsing.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_utils.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-aarch64-3.10/src/oxli/read_parsers.o build/temp.linux-aarch64-3.10/src/oxli/kmer_hash.o build/temp.linux-aarch64-3.10/src/oxli/hashtable.o build/temp.linux-aarch64-3.10/src/oxli/hashgraph.o build/temp.linux-aarch64-3.10/src/oxli/labelhash.o build/temp.linux-aarch64-3.10/src/oxli/subset.o build/temp.linux-aarch64-3.10/src/oxli/read_aligner.o build/temp.linux-aarch64-3.10/src/oxli/hllcounter.o build/temp.linux-aarch64-3.10/src/oxli/traversal.o build/temp.linux-aarch64-3.10/src/oxli/kmer_filters.o build/temp.linux-aarch64-3.10/src/oxli/assembler.o build/temp.linux-aarch64-3.10/src/oxli/alphabets.o build/temp.linux-aarch64-3.10/src/oxli/storage.o build/temp.linux-aarch64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-aarch64-3.10/khmer/_oxli/parsing.cpython-310-aarch64-linux-gnu.so -fopenmp building 'khmer._oxli.hashing' extension aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c khmer/_oxli/hashing.cpp -o build/temp.linux-aarch64-3.10/khmer/_oxli/hashing.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.10/khmer/_oxli/hashing.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_utils.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-aarch64-3.10/src/oxli/read_parsers.o build/temp.linux-aarch64-3.10/src/oxli/kmer_hash.o build/temp.linux-aarch64-3.10/src/oxli/hashtable.o build/temp.linux-aarch64-3.10/src/oxli/hashgraph.o build/temp.linux-aarch64-3.10/src/oxli/labelhash.o build/temp.linux-aarch64-3.10/src/oxli/subset.o build/temp.linux-aarch64-3.10/src/oxli/read_aligner.o build/temp.linux-aarch64-3.10/src/oxli/hllcounter.o build/temp.linux-aarch64-3.10/src/oxli/traversal.o build/temp.linux-aarch64-3.10/src/oxli/kmer_filters.o build/temp.linux-aarch64-3.10/src/oxli/assembler.o build/temp.linux-aarch64-3.10/src/oxli/alphabets.o build/temp.linux-aarch64-3.10/src/oxli/storage.o build/temp.linux-aarch64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-aarch64-3.10/khmer/_oxli/hashing.cpython-310-aarch64-linux-gnu.so -fopenmp building 'khmer._oxli.graphs' extension aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c khmer/_oxli/graphs.cpp -o build/temp.linux-aarch64-3.10/khmer/_oxli/graphs.o -O3 -std=c++11 -pedantic -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:740: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/graphs.cpp:620: note: this is the location of the previous definition 620 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/graphs.cpp:627: note: this is the location of the previous definition 627 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/graphs.cpp:624: note: this is the location of the previous definition 624 | #define PyInt_FromLong PyLong_FromLong | aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.10/khmer/_oxli/graphs.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_utils.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-aarch64-3.10/src/oxli/read_parsers.o build/temp.linux-aarch64-3.10/src/oxli/kmer_hash.o build/temp.linux-aarch64-3.10/src/oxli/hashtable.o build/temp.linux-aarch64-3.10/src/oxli/hashgraph.o build/temp.linux-aarch64-3.10/src/oxli/labelhash.o build/temp.linux-aarch64-3.10/src/oxli/subset.o build/temp.linux-aarch64-3.10/src/oxli/read_aligner.o build/temp.linux-aarch64-3.10/src/oxli/hllcounter.o build/temp.linux-aarch64-3.10/src/oxli/traversal.o build/temp.linux-aarch64-3.10/src/oxli/kmer_filters.o build/temp.linux-aarch64-3.10/src/oxli/assembler.o build/temp.linux-aarch64-3.10/src/oxli/alphabets.o build/temp.linux-aarch64-3.10/src/oxli/storage.o build/temp.linux-aarch64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-aarch64-3.10/khmer/_oxli/graphs.cpython-310-aarch64-linux-gnu.so -fopenmp building 'khmer._oxli.utils' extension aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c khmer/_oxli/utils.cpp -o build/temp.linux-aarch64-3.10/khmer/_oxli/utils.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.10/khmer/_oxli/utils.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_utils.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-aarch64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-aarch64-3.10/src/oxli/read_parsers.o build/temp.linux-aarch64-3.10/src/oxli/kmer_hash.o build/temp.linux-aarch64-3.10/src/oxli/hashtable.o build/temp.linux-aarch64-3.10/src/oxli/hashgraph.o build/temp.linux-aarch64-3.10/src/oxli/labelhash.o build/temp.linux-aarch64-3.10/src/oxli/subset.o build/temp.linux-aarch64-3.10/src/oxli/read_aligner.o build/temp.linux-aarch64-3.10/src/oxli/hllcounter.o build/temp.linux-aarch64-3.10/src/oxli/traversal.o build/temp.linux-aarch64-3.10/src/oxli/kmer_filters.o build/temp.linux-aarch64-3.10/src/oxli/assembler.o build/temp.linux-aarch64-3.10/src/oxli/alphabets.o build/temp.linux-aarch64-3.10/src/oxli/storage.o build/temp.linux-aarch64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-aarch64-3.10/khmer/_oxli/utils.cpython-310-aarch64-linux-gnu.so -fopenmp copying build/lib.linux-aarch64-3.10/khmer/_khmer.cpython-310-aarch64-linux-gnu.so -> khmer copying build/lib.linux-aarch64-3.10/khmer/_oxli/assembly.cpython-310-aarch64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-aarch64-3.10/khmer/_oxli/parsing.cpython-310-aarch64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-aarch64-3.10/khmer/_oxli/hashing.cpython-310-aarch64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-aarch64-3.10/khmer/_oxli/graphs.cpython-310-aarch64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-aarch64-3.10/khmer/_oxli/utils.cpython-310-aarch64-linux-gnu.so -> khmer/_oxli Creating /<>/fakehome/.local/lib/python3.10/site-packages/khmer.egg-link (link to .) Adding khmer 2.1.2 to easy-install.pth file Installing annotate-partitions.py script to /<>/fakehome/.local/bin Installing find-knots.py script to /<>/fakehome/.local/bin Installing load-into-counting.py script to /<>/fakehome/.local/bin Installing partition-graph.py script to /<>/fakehome/.local/bin Installing trim-low-abund.py script to /<>/fakehome/.local/bin Installing filter-stoptags.py script to /<>/fakehome/.local/bin Installing extract-long-sequences.py script to /<>/fakehome/.local/bin Installing normalize-by-median.py script to /<>/fakehome/.local/bin Installing readstats.py script to /<>/fakehome/.local/bin Installing make-initial-stoptags.py script to /<>/fakehome/.local/bin Installing unique-kmers.py script to /<>/fakehome/.local/bin Installing merge-partitions.py script to /<>/fakehome/.local/bin Installing filter-abund.py script to /<>/fakehome/.local/bin Installing load-graph.py script to /<>/fakehome/.local/bin Installing abundance-dist-single.py script to /<>/fakehome/.local/bin Installing extract-paired-reads.py script to /<>/fakehome/.local/bin Installing interleave-reads.py script to /<>/fakehome/.local/bin Installing do-partition.py script to /<>/fakehome/.local/bin Installing sample-reads-randomly.py script to /<>/fakehome/.local/bin Installing abundance-dist.py script to /<>/fakehome/.local/bin Installing extract-partitions.py script to /<>/fakehome/.local/bin Installing fastq-to-fasta.py script to /<>/fakehome/.local/bin Installing split-paired-reads.py script to /<>/fakehome/.local/bin Installing count-median.py script to /<>/fakehome/.local/bin Installing filter-abund-single.py script to /<>/fakehome/.local/bin Installed /<> Processing dependencies for khmer==2.1.2 Searching for screed==1.0.5 Best match: screed 1.0.5 Adding screed 1.0.5 to easy-install.pth file Installing screed script to /<>/fakehome/.local/bin Using /usr/lib/python3/dist-packages Searching for Cython==0.29.30 Best match: Cython 0.29.30 Adding Cython 0.29.30 to easy-install.pth file Using /usr/lib/python3/dist-packages Finished processing dependencies for khmer==2.1.2 /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead warnings.warn( running build_sphinx Running Sphinx v4.5.0 making output directory... done building [mo]: targets for 0 po files that are out of date building [html]: targets for 41 source files that are out of date updating environment: [new config] 41 added, 0 changed, 0 removed reading sources... [ 2%] LICENSE reading sources... [ 4%] citations reading sources... [ 7%] contributors reading sources... [ 9%] dev/CODE_OF_CONDUCT reading sources... [ 12%] dev/a-quick-guide-to-testing reading sources... [ 14%] dev/binary-file-formats reading sources... [ 17%] dev/codebase-guide reading sources... [ 19%] dev/development reading sources... [ 21%] dev/for-khmer-developers reading sources... [ 24%] dev/getting-started reading sources... [ 26%] dev/guidelines-continued-dev reading sources... [ 29%] dev/hackathon reading sources... [ 31%] dev/index reading sources... [ 34%] dev/python-api reading sources... [ 36%] dev/release reading sources... [ 39%] dev/scripts-and-sandbox reading sources... [ 41%] index reading sources... [ 43%] introduction reading sources... [ 46%] release-notes/index reading sources... [ 48%] release-notes/release-1.0 reading sources... [ 51%] release-notes/release-1.0.1 reading sources... [ 53%] release-notes/release-1.1 reading sources... [ 56%] release-notes/release-1.2 reading sources... [ 58%] release-notes/release-1.3 reading sources... [ 60%] release-notes/release-1.4 reading sources... [ 63%] release-notes/release-2.0 reading sources... [ 65%] release-notes/release-2.1 reading sources... [ 68%] roadmap reading sources... [ 70%] user/api-examples reading sources... [ 73%] user/biblio reading sources... [ 75%] user/blog-posts reading sources... [ 78%] user/choosing-table-sizes reading sources... [ 80%] user/examples reading sources... [ 82%] user/galaxy reading sources... [ 85%] user/getting-help reading sources... [ 87%] user/guide reading sources... [ 90%] user/index reading sources... [ 92%] user/install reading sources... [ 95%] user/known-issues reading sources... [ 97%] user/partitioning-big-data reading sources... [100%] user/scripts looking for now-outdated files... none found pickling environment... done checking consistency... /<>/doc/dev/hackathon.rst: WARNING: document isn't included in any toctree /<>/doc/dev/python-api.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 2%] LICENSE writing output... [ 4%] citations writing output... [ 7%] contributors writing output... [ 9%] dev/CODE_OF_CONDUCT writing output... [ 12%] dev/a-quick-guide-to-testing writing output... [ 14%] dev/binary-file-formats writing output... [ 17%] dev/codebase-guide writing output... [ 19%] dev/development writing output... [ 21%] dev/for-khmer-developers writing output... [ 24%] dev/getting-started writing output... [ 26%] dev/guidelines-continued-dev writing output... [ 29%] dev/hackathon writing output... [ 31%] dev/index writing output... [ 34%] dev/python-api writing output... [ 36%] dev/release writing output... [ 39%] dev/scripts-and-sandbox writing output... [ 41%] index writing output... [ 43%] introduction writing output... [ 46%] release-notes/index writing output... [ 48%] release-notes/release-1.0 writing output... [ 51%] release-notes/release-1.0.1 writing output... [ 53%] release-notes/release-1.1 writing output... [ 56%] release-notes/release-1.2 writing output... [ 58%] release-notes/release-1.3 writing output... [ 60%] release-notes/release-1.4 writing output... [ 63%] release-notes/release-2.0 writing output... [ 65%] release-notes/release-2.1 writing output... [ 68%] roadmap writing output... [ 70%] user/api-examples writing output... [ 73%] user/biblio writing output... [ 75%] user/blog-posts writing output... [ 78%] user/choosing-table-sizes writing output... [ 80%] user/examples writing output... [ 82%] user/galaxy writing output... [ 85%] user/getting-help writing output... [ 87%] user/guide writing output... [ 90%] user/index writing output... [ 92%] user/install writing output... [ 95%] user/known-issues writing output... [ 97%] user/partitioning-big-data writing output... [100%] user/scripts /<>/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: load-into-counting.py -N /<>/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: load-into-counting.py --n_tables /<>/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: load-into-counting.py -x /<>/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: load-into-counting.py --max-tablesize /<>/doc/user/scripts.rst:79: WARNING: unknown option: -x /<>/doc/user/scripts.rst:79: WARNING: unknown option: -N /<>/doc/user/scripts.rst:87: WARNING: unknown option: -x /<>/doc/user/scripts.rst:87: WARNING: unknown option: -N generating indices... genindex done writing additional pages... search done copying images... [ 50%] user/partitioning-workflow.png copying images... [100%] user/artifact-removal.png copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 10 warnings. The HTML pages are in build/sphinx/html. asciidoctor --backend manpage -a reproducible debian/khmer.1.adoc cd src/oxli && /usr/bin/make clean all make[2]: Entering directory '/<>/src/oxli' rm -f *.o *.a *.so* oxli.pc g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o hashtable.o hashtable.cc hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: hashtable.cc:512:1: required from here hashtable.cc:103:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 103 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: hashtable.cc:529:1: required from here hashtable.cc:133:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 133 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o hashgraph.o hashgraph.cc g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o hllcounter.o hllcounter.cc hllcounter.cc: In instantiation of ‘void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: hllcounter.cc:524:1: required from here hllcounter.cc:428:40: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 428 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o kmer_hash.o kmer_hash.cc g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o labelhash.o labelhash.cc g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o traversal.o traversal.cc In file included from traversal.cc:39: traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]’: traversal.cc:202:5: required from here ../../include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ ../../include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]’: traversal.cc:203:5: required from here ../../include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ ../../include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o read_aligner.o read_aligner.cc g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o read_parsers.o read_parsers.cc In file included from ../../third-party/seqan/core/include/seqan/basic.h:62, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from ../../third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/modifier.h:66, from ../../third-party/seqan/core/include/seqan/file.h:48, from ../../third-party/seqan/core/include/seqan/stream.h:70, from ../../third-party/seqan/core/include/seqan/seq_io.h:45: ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:68:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 68 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from read_parsers.cc:38: /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:91:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 91 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:169:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 169 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:178:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 178 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:188:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 188 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:198:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 198 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:208:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 208 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:217:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 217 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:229:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/file.h:117: ../../third-party/seqan/core/include/seqan/file/string_external.h:1316:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1316 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/graph_algorithms.h:46, from ../../third-party/seqan/core/include/seqan/graph_align.h:47, from ../../third-party/seqan/core/include/seqan/align.h:54, from ../../third-party/seqan/core/include/seqan/store.h:38, from ../../third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from ../../third-party/seqan/core/include/seqan/seq_io.h:83: ../../third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:340:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 340 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/graph_algorithms.h:47: ../../third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm.h:643:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 643 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/align.h:79: ../../third-party/seqan/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/align.h:116: ../../third-party/seqan/core/include/seqan/align/dp_cell_affine.h: In member function ‘seqan::DPCell_ >& seqan::DPCell_ >::operator=(const seqan::DPCell_ >&)’: ../../third-party/seqan/core/include/seqan/align/dp_cell_affine.h:84:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 84 | if (this != &other) | ^~ ../../third-party/seqan/core/include/seqan/align/dp_cell_affine.h:86:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 86 | _horizontalScore = other._horizontalScore; | ^~~~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/align.h:166: ../../third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: ../../third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ ../../third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from ../../third-party/seqan/core/include/seqan/align.h:174: ../../third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: ../../third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ ../../third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from ../../third-party/seqan/core/include/seqan/bam_io.h:107, from ../../third-party/seqan/core/include/seqan/store.h:41: ../../third-party/seqan/core/include/seqan/bam_io/bam_stream.h: At global scope: ../../third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/store.h:59: ../../third-party/seqan/core/include/seqan/store/store_align.h:322:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 322 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/store/store_align.h:332:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 332 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/store/store_align.h:342:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/store/store_align.h:352:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/store/store_align.h:362:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/store/store_align.h:372:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/store.h:61: ../../third-party/seqan/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: ../../third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1733 | if (alignQualityStoreLengthPre == 0u) | ^~ ../../third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o subset.o subset.cc subset.cc: In member function ‘size_t oxli::SubsetPartition::output_partitioned_file(const std::string&, const std::string&, bool, oxli::CallbackFn, void*)’: subset.cc:136:24: warning: unused variable ‘ksize’ [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o kmer_filters.o kmer_filters.cc g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o assembler.o assembler.cc In file included from assembler.cc:38: ../../include/oxli/assembler.hh: In constructor ‘oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)’: ../../include/oxli/assembler.hh:80:23: warning: ‘oxli::LinearAssembler::graph’ will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ ../../include/oxli/assembler.hh:79:16: warning: ‘oxli::WordLength oxli::LinearAssembler::_ksize’ [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ assembler.cc: In destructor ‘oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()’: assembler.cc:189:5: warning: deleting object of polymorphic class type ‘oxli::LinearAssembler’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ ../../include/oxli/assembler.hh: In constructor ‘oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)’: ../../include/oxli/assembler.hh:158:16: warning: ‘oxli::JunctionCountAssembler::_ksize’ will be initialized after [-Wreorder] 158 | WordLength _ksize; | ^~~~~~ ../../include/oxli/assembler.hh:153:15: warning: ‘oxli::Traverser oxli::JunctionCountAssembler::traverser’ [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ ../../include/oxli/assembler.hh:153:15: warning: ‘oxli::JunctionCountAssembler::traverser’ will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ ../../include/oxli/assembler.hh:151:21: warning: ‘oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm’ [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o alphabets.o alphabets.cc g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -c -o murmur3.o ../../third-party/smhasher/MurmurHash3.cc g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o storage.o storage.cc g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lz -lbz2 -Wl,-soname=liboxli.so.1 -shared -o liboxli.so.1 hashtable.o hashgraph.o hllcounter.o kmer_hash.o labelhash.o traversal.o read_aligner.o read_parsers.o subset.o kmer_filters.o assembler.o alphabets.o murmur3.o storage.o ln -sf liboxli.so.1 liboxli.so ar rcs liboxli.a hashtable.o hashgraph.o hllcounter.o kmer_hash.o labelhash.o traversal.o read_aligner.o read_parsers.o subset.o kmer_filters.o assembler.o alphabets.o murmur3.o storage.o ranlib liboxli.a sed -e 's,@prefix@,/usr/local,' -e 's,@VERSION@,,' oxli.pc.in >oxli.pc make[2]: Leaving directory '/<>/src/oxli' make[1]: Leaving directory '/<>' rm -f debian/khmer.debhelper.log debian/liboxli-dev.debhelper.log debian/liboxli1.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/<>' dh_auto_install install -d /<>/khmer-2.1.2\+dfsg/debian/tmp pybuild --install -i python{version} -p 3.10 --dest-dir /<>/khmer-2.1.2\+dfsg/debian/tmp I: pybuild base:240: /usr/bin/python3 setup.py install --root /<>/debian/khmer '--install-scripts=/usr/lib/khmer/bin' /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead warnings.warn( running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running egg_info writing khmer.egg-info/PKG-INFO writing dependency_links to khmer.egg-info/dependency_links.txt writing requirements to khmer.egg-info/requires.txt writing top-level names to khmer.egg-info/top_level.txt reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.hh' under directory 'khmer' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching '*.c' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '[Mm]akefile*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'khmer.egg-info/SOURCES.txt' copying khmer/_oxli/assembly.cpp -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.cpp -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.cpp -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.cpp -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/utils.cpp -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli UPDATING /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_version.py set /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_version.py to '2.1.2' running build_ext skipping 'khmer/_oxli/assembly.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/parsing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/hashing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/graphs.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/utils.cpp' Cython extension (up-to-date) building 'khmer._khmer' extension aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_countgraph.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_counttable.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_graphlabels.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashgraph.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashset.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashtable.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hllcounter.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_nodegraph.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_nodetable.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_readaligner.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_smallcountgraph.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_smallcounttable.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_subsetpartition.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_utils.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/alphabets.cc -o build/temp.linux-arm64-3.10/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/assembler.cc -o build/temp.linux-arm64-3.10/src/oxli/assembler.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor ‘oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)’: include/oxli/assembler.hh:80:23: warning: ‘oxli::LinearAssembler::graph’ will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ include/oxli/assembler.hh:79:16: warning: ‘oxli::WordLength oxli::LinearAssembler::_ksize’ [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor ‘oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()’: src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type ‘oxli::LinearAssembler’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh: In constructor ‘oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)’: include/oxli/assembler.hh:158:16: warning: ‘oxli::JunctionCountAssembler::_ksize’ will be initialized after [-Wreorder] 158 | WordLength _ksize; | ^~~~~~ include/oxli/assembler.hh:153:15: warning: ‘oxli::Traverser oxli::JunctionCountAssembler::traverser’ [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh:153:15: warning: ‘oxli::JunctionCountAssembler::traverser’ will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ include/oxli/assembler.hh:151:21: warning: ‘oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm’ [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hashgraph.cc -o build/temp.linux-arm64-3.10/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hashtable.cc -o build/temp.linux-arm64-3.10/src/oxli/hashtable.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hashtable.cc:512:1: required from here src/oxli/hashtable.cc:103:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 103 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hashtable.cc:529:1: required from here src/oxli/hashtable.cc:133:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 133 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hllcounter.cc -o build/temp.linux-arm64-3.10/src/oxli/hllcounter.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hllcounter.cc: In instantiation of ‘void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hllcounter.cc:524:1: required from here src/oxli/hllcounter.cc:428:40: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 428 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/kmer_filters.cc -o build/temp.linux-arm64-3.10/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/kmer_hash.cc -o build/temp.linux-arm64-3.10/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/labelhash.cc -o build/temp.linux-arm64-3.10/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/read_aligner.cc -o build/temp.linux-arm64-3.10/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/read_parsers.cc -o build/temp.linux-arm64-3.10/src/oxli/read_parsers.o -O3 -std=c++11 -pedantic -fopenmp In file included from third-party/seqan/core/include/seqan/basic.h:62, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/modifier.h:66, from third-party/seqan/core/include/seqan/file.h:48, from third-party/seqan/core/include/seqan/stream.h:70, from third-party/seqan/core/include/seqan/seq_io.h:45: third-party/seqan/core/include/seqan/modifier/modifier_functors.h:68:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 68 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from src/oxli/read_parsers.cc:38: /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:91:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 91 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:169:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 169 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:178:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 178 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:188:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 188 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:198:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 198 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:208:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 208 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:217:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 217 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:229:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/file.h:117: third-party/seqan/core/include/seqan/file/string_external.h:1316:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1316 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/graph_algorithms.h:46, from third-party/seqan/core/include/seqan/graph_align.h:47, from third-party/seqan/core/include/seqan/align.h:54, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83: third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:340:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 340 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/graph_algorithms.h:47: third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm.h:643:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 643 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:79: third-party/seqan/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:116: third-party/seqan/core/include/seqan/align/dp_cell_affine.h: In member function ‘seqan::DPCell_ >& seqan::DPCell_ >::operator=(const seqan::DPCell_ >&)’: third-party/seqan/core/include/seqan/align/dp_cell_affine.h:84:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 84 | if (this != &other) | ^~ third-party/seqan/core/include/seqan/align/dp_cell_affine.h:86:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 86 | _horizontalScore = other._horizontalScore; | ^~~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:166: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from third-party/seqan/core/include/seqan/align.h:174: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41: third-party/seqan/core/include/seqan/bam_io/bam_stream.h: At global scope: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:59: third-party/seqan/core/include/seqan/store/store_align.h:322:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 322 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:332:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 332 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:342:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:352:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:362:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:372:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61: third-party/seqan/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1733 | if (alignQualityStoreLengthPre == 0u) | ^~ third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/storage.cc -o build/temp.linux-arm64-3.10/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/subset.cc -o build/temp.linux-arm64-3.10/src/oxli/subset.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/subset.cc: In member function ‘size_t oxli::SubsetPartition::output_partitioned_file(const std::string&, const std::string&, bool, oxli::CallbackFn, void*)’: src/oxli/subset.cc:136:24: warning: unused variable ‘ksize’ [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/traversal.cc -o build/temp.linux-arm64-3.10/src/oxli/traversal.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:202:5: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:203:5: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-arm64-3.10/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-arm64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-arm64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-arm64-3.10/src/khmer/_cpy_utils.o build/temp.linux-arm64-3.10/src/oxli/alphabets.o build/temp.linux-arm64-3.10/src/oxli/assembler.o build/temp.linux-arm64-3.10/src/oxli/hashgraph.o build/temp.linux-arm64-3.10/src/oxli/hashtable.o build/temp.linux-arm64-3.10/src/oxli/hllcounter.o build/temp.linux-arm64-3.10/src/oxli/kmer_filters.o build/temp.linux-arm64-3.10/src/oxli/kmer_hash.o build/temp.linux-arm64-3.10/src/oxli/labelhash.o build/temp.linux-arm64-3.10/src/oxli/read_aligner.o build/temp.linux-arm64-3.10/src/oxli/read_parsers.o build/temp.linux-arm64-3.10/src/oxli/storage.o build/temp.linux-arm64-3.10/src/oxli/subset.o build/temp.linux-arm64-3.10/src/oxli/traversal.o build/temp.linux-arm64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_khmer.cpython-310-aarch64-linux-gnu.so -fopenmp running build_scripts running install_lib creating /<>/debian/khmer creating /<>/debian/khmer/usr creating /<>/debian/khmer/usr/lib creating /<>/debian/khmer/usr/lib/python3.10 creating /<>/debian/khmer/usr/lib/python3.10/dist-packages creating /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/trimming.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/khmer_args.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/kfile.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer creating /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.cpp -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/utils.cpython-310-aarch64-linux-gnu.so -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.cpython-310-aarch64-linux-gnu.so -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/graphs.pxd -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/parsing.pxd -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hllcounter.pxd -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/traversal.pxd -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.pyx -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.cpp -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/utils.pxd -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/parsing.pyx -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/parsing.cpp -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.pyx -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/graphs.pyx -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/utils.cpp -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.pxd -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/utils.pyx -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/parsing.cpython-310-aarch64-linux-gnu.so -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/oxli_types.pxd -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/__init__.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.cpython-310-aarch64-linux-gnu.so -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.pxd -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/graphs.cpython-310-aarch64-linux-gnu.so -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/graphs.cpp -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/khmer_logger.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_khmer.cpython-310-aarch64-linux-gnu.so -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer creating /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_cython_parsing.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_banding.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_script_arguments.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_labelhash.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_cython_assembly.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_functions.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_lump.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests creating /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-3.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-multi.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/badversion-k12.ct -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-fastq-reads.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-sweep-contigs.fp -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/readaligner-default.json -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken.fq.badright -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/all-A.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.malformat.fq.2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/old-style-format-w-comments.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/100-reads.fq.gz -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/filter-test-B.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fa.gz -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken2.fq.1 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.bz2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-fastq-n-reads.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken4.fq.1 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-sweep-reads.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fq.bz2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/badversion-k32.stoptags -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/filter-test-A.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/real-partition-small.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-large.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/goodversion-k12.ht -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/readaligner-k12.json -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken3.fq.1 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/casava_18-pe.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/dn-test-none-paired.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-filter-abund-Ns.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/fakelump.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken2.fq.2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed-2.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/valid-read-testing.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-graph5.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-graph.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-empty.fa.bz2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken.fq.2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-short.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fa.bz2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fa.part -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.gz -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-output-partitions.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/unclean-reads.fastq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-slash1.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/empty-file.gz -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-fastq-reads.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/badversion-k32.tagset -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-labels.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/dn-test-all-paired-all-keep.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fa.se -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fq.pe -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-overlap1.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-graph2.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-overlap2.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken4.fq.2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired_one.base.dif.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/real-partition-tiny.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/goodversion-k32.stoptags -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-paired.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/empty-file.bz2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/empty-file -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken3.fq.2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/README.rst -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fq.2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/multi-output.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.paired.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-transcript.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed-witherror.fa.pe -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/truncated.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/100-reads.fq.bz2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/normC20k20.ct -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-X2.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/single-read.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fa.1 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/bogus.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/goodversion-k32.tagset -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/badversion-k12.ht -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fq.1 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.malformat.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-error-reads.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/simple-genome.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fq.se -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken.fq.paired_bad -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-paired.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-reads.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-31-c.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-slash1.fq.1 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/single-read.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.odd.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/combine_parts_1.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fq.gz -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-sweep-reads.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken.fq.badleft -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/dn-test-some-paired-all-keep.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed-broken.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/banding-reads.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.gz -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-reads.fq.gz -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.paired2.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.even.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/fakelump.fa.stoptags.txt -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken.fq.1 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-impaired.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-empty.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.bz2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fa.2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/goodversion-k12.ht.gz -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-slash1.fq.2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/simple-genome-reads.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fa.pe -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/biglump-random-20-a.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-b.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-reads.fq.bz2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/graph_features.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_nibblestorage.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_hashset.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_sandbox_scripts.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_nodegraph.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_version.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_read_aligner.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_countgraph.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_read_handling.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_threaded_sequence_processor.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/.gitignore -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_hll.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_counttable.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_normalize_by_median.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_scripts.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_subset_graph.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__init__.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/khmer_tst_utils.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_cpython_hierarchy.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_sequence_validation.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_filter_abund.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_counting_single.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_script_output.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_read_parsers.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_tabletype.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_oxli_functions.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_streaming_io.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_graph.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_version.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/__init__.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/utils.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/thread_utils.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer creating /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/oxli/build_graph.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/oxli/functions.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/oxli/__init__.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/oxli/partition.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/trimming.py to trimming.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/khmer_args.py to khmer_args.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/kfile.py to kfile.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/khmer_logger.py to khmer_logger.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_cython_parsing.py to test_cython_parsing.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_banding.py to test_banding.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_script_arguments.py to test_script_arguments.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_labelhash.py to test_labelhash.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_cython_assembly.py to test_cython_assembly.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_functions.py to test_functions.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_lump.py to test_lump.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/graph_features.py to graph_features.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_nibblestorage.py to test_nibblestorage.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_hashset.py to test_hashset.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_sandbox_scripts.py to test_sandbox_scripts.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_nodegraph.py to test_nodegraph.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_version.py to test_version.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_read_aligner.py to test_read_aligner.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_countgraph.py to test_countgraph.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_read_handling.py to test_read_handling.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_threaded_sequence_processor.py to test_threaded_sequence_processor.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_hll.py to test_hll.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_counttable.py to test_counttable.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_normalize_by_median.py to test_normalize_by_median.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_scripts.py to test_scripts.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py to test_subset_graph.cpython-310.pyc /usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py:61: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py:82: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py:278: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py:476: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py:509: SyntaxWarning: "is" with a literal. Did you mean "=="? byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/khmer_tst_utils.py to khmer_tst_utils.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_cpython_hierarchy.py to test_cpython_hierarchy.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_sequence_validation.py to test_sequence_validation.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_filter_abund.py to test_filter_abund.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_counting_single.py to test_counting_single.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_script_output.py to test_script_output.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_read_parsers.py to test_read_parsers.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_tabletype.py to test_tabletype.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_oxli_functions.py to test_oxli_functions.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_streaming_io.py to test_streaming_io.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_graph.py to test_graph.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_version.py to _version.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/utils.py to utils.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/thread_utils.py to thread_utils.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli/build_graph.py to build_graph.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli/functions.py to functions.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli/partition.py to partition.cpython-310.pyc running install_egg_info Copying khmer.egg-info to /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer-2.1.2.egg-info Skipping SOURCES.txt running install_scripts creating /<>/debian/khmer/usr/lib/khmer creating /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/annotate-partitions.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/find-knots.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/load-into-counting.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/partition-graph.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/trim-low-abund.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/filter-stoptags.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/extract-long-sequences.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/normalize-by-median.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/readstats.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/make-initial-stoptags.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/unique-kmers.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/merge-partitions.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/filter-abund.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/load-graph.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/abundance-dist-single.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/extract-paired-reads.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/interleave-reads.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/do-partition.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/sample-reads-randomly.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/abundance-dist.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/extract-partitions.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/fastq-to-fasta.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/split-paired-reads.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/count-median.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/filter-abund-single.py -> /<>/debian/khmer/usr/lib/khmer/bin changing mode of /<>/debian/khmer/usr/lib/khmer/bin/annotate-partitions.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/find-knots.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/load-into-counting.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/partition-graph.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/trim-low-abund.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/filter-stoptags.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/extract-long-sequences.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/normalize-by-median.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/readstats.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/make-initial-stoptags.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/unique-kmers.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/merge-partitions.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/filter-abund.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/load-graph.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/abundance-dist-single.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/extract-paired-reads.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/interleave-reads.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/do-partition.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/sample-reads-randomly.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/abundance-dist.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/extract-partitions.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/fastq-to-fasta.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/split-paired-reads.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/count-median.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/filter-abund-single.py to 755 PYBUILD_SYSTEM=custom \ PYBUILD_TEST_ARGS="cd {dir}; export PATH={destdir}/usr/lib/khmer/bin:$PATH ; \ cd {build_dir}; export PYTHONPATH=$(pwd); {interpreter} -m pytest \ -m 'not known_failing and not jenkins and not huge and not noroot'\ -q" dh_auto_test pybuild --test --test-pytest -i python{version} -p 3.10 I: pybuild base:240: cd /<>; export PATH=/<>/debian/khmer/usr/lib/khmer/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games ; cd /<>/.pybuild/cpython3_3.10_khmer/build; export PYTHONPATH=/<>; python3.10 -m pytest -m 'not known_failing and not jenkins and not huge and not noroot' -q ============================= test session starts ============================== platform linux -- Python 3.10.6, pytest-7.1.2, pluggy-1.0.0+repack rootdir: /<>, configfile: pytest.ini collected 2732 items / 52 deselected / 2680 selected khmer/tests/test_banding.py ............ [ 0%] khmer/tests/test_countgraph.py ......................................... [ 1%] .................................................. [ 3%] khmer/tests/test_counting_single.py ......................... [ 4%] khmer/tests/test_counttable.py .......... [ 5%] khmer/tests/test_cpython_hierarchy.py .... [ 5%] khmer/tests/test_cython_assembly.py .................................... [ 6%] ........................................................................ [ 9%] ........................................................................ [ 12%] ........................................................................ [ 14%] ........................................................................ [ 17%] ......... [ 17%] khmer/tests/test_cython_parsing.py ..................................... [ 19%] .... [ 19%] khmer/tests/test_filter_abund.py ................... [ 19%] khmer/tests/test_functions.py .................. [ 20%] khmer/tests/test_graph.py ............................ [ 21%] khmer/tests/test_hashset.py ............. [ 22%] khmer/tests/test_hll.py ...................... [ 22%] khmer/tests/test_labelhash.py ................. [ 23%] khmer/tests/test_lump.py ...... [ 23%] khmer/tests/test_nibblestorage.py ..... [ 24%] khmer/tests/test_nodegraph.py .......................................... [ 25%] ........................ [ 26%] khmer/tests/test_normalize_by_median.py ................................ [ 27%] ...... [ 27%] khmer/tests/test_oxli_functions.py .... [ 28%] khmer/tests/test_read_aligner.py ..................x. [ 28%] khmer/tests/test_read_handling.py ................................ [ 30%] khmer/tests/test_read_parsers.py .............................. [ 31%] khmer/tests/test_sandbox_scripts.py sssssssssss [ 31%] khmer/tests/test_script_arguments.py ............................ [ 32%] khmer/tests/test_script_output.py ........... [ 32%] khmer/tests/test_scripts.py ............................................ [ 34%] ........................................................................ [ 37%] .............................. [ 38%] khmer/tests/test_sequence_validation.py ................................ [ 39%] ............ [ 40%] khmer/tests/test_streaming_io.py ............................ [ 41%] khmer/tests/test_subset_graph.py ........................... [ 42%] khmer/tests/test_tabletype.py .....................................s.s.s [ 43%] ........................................................................ [ 46%] ........................................................................ [ 49%] .................. [ 49%] khmer/tests/test_threaded_sequence_processor.py ...... [ 49%] khmer/tests/test_version.py . [ 50%] tests/test_banding.py ............ [ 50%] tests/test_countgraph.py ............................................... [ 52%] ............................................ [ 53%] tests/test_counting_single.py ......................... [ 54%] tests/test_counttable.py .......... [ 55%] tests/test_cpython_hierarchy.py .... [ 55%] tests/test_cython_assembly.py .......................................... [ 56%] ........................................................................ [ 59%] ........................................................................ [ 62%] ........................................................................ [ 64%] ........................................................................ [ 67%] ... [ 67%] tests/test_cython_parsing.py ......................................... [ 69%] tests/test_filter_abund.py ................... [ 69%] tests/test_functions.py .................. [ 70%] tests/test_graph.py ............................ [ 71%] tests/test_hashset.py ............. [ 72%] tests/test_hll.py ...................... [ 72%] tests/test_labelhash.py ................. [ 73%] tests/test_lump.py ...... [ 73%] tests/test_nibblestorage.py ..... [ 74%] tests/test_nodegraph.py ................................................ [ 75%] .................. [ 76%] tests/test_normalize_by_median.py ...................................... [ 77%] [ 77%] tests/test_oxli_functions.py .... [ 78%] tests/test_read_aligner.py ..................x. [ 78%] tests/test_read_handling.py ................................ [ 80%] tests/test_read_parsers.py .............................. [ 81%] tests/test_sandbox_scripts.py sssssssssss [ 81%] tests/test_script_arguments.py ............................ [ 82%] tests/test_script_output.py ........... [ 82%] tests/test_scripts.py .................................................. [ 84%] ........................................................................ [ 87%] ........................ [ 88%] tests/test_sequence_validation.py ...................................... [ 89%] ...... [ 90%] tests/test_streaming_io.py ............................ [ 91%] tests/test_subset_graph.py ........................... [ 92%] tests/test_tabletype.py .....................................s.s.s...... [ 93%] ........................................................................ [ 96%] ........................................................................ [ 99%] ............ [ 99%] tests/test_threaded_sequence_processor.py ...... [ 99%] tests/test_version.py . [100%] === 2650 passed, 28 skipped, 52 deselected, 2 xfailed in 1238.60s (0:20:38) ==== rm -fr -- /tmp/dh-xdg-rundir-GcgTasO9 make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild rm -f -- debian/khmer.substvars debian/liboxli1.substvars debian/liboxli-dev.substvars rm -fr -- debian/.debhelper/generated/khmer/ debian/khmer/ debian/tmp/ debian/.debhelper/generated/liboxli1/ debian/liboxli1/ debian/.debhelper/generated/liboxli-dev/ debian/liboxli-dev/ dh_auto_install -a -O--buildsystem=pybuild install -d /<>/khmer-2.1.2\+dfsg/debian/tmp pybuild --install -i python{version} -p 3.10 --dest-dir /<>/khmer-2.1.2\+dfsg/debian/tmp I: pybuild base:240: /usr/bin/python3 setup.py install --root /<>/debian/khmer '--install-scripts=/usr/lib/khmer/bin' /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead warnings.warn( running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running egg_info writing khmer.egg-info/PKG-INFO writing dependency_links to khmer.egg-info/dependency_links.txt writing requirements to khmer.egg-info/requires.txt writing top-level names to khmer.egg-info/top_level.txt reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.hh' under directory 'khmer' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching '*.c' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '[Mm]akefile*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'khmer.egg-info/SOURCES.txt' UPDATING /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_version.py set /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_version.py to '2.1.2' running build_ext skipping 'khmer/_oxli/assembly.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/parsing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/hashing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/graphs.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/utils.cpp' Cython extension (up-to-date) building 'khmer._khmer' extension aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_countgraph.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_counttable.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_graphlabels.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashgraph.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashset.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashtable.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hllcounter.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_nodegraph.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_nodetable.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_readaligner.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_smallcountgraph.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_smallcounttable.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_subsetpartition.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_utils.cc -o build/temp.linux-arm64-3.10/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/alphabets.cc -o build/temp.linux-arm64-3.10/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/assembler.cc -o build/temp.linux-arm64-3.10/src/oxli/assembler.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor ‘oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)’: include/oxli/assembler.hh:80:23: warning: ‘oxli::LinearAssembler::graph’ will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ include/oxli/assembler.hh:79:16: warning: ‘oxli::WordLength oxli::LinearAssembler::_ksize’ [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor ‘oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()’: src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type ‘oxli::LinearAssembler’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh: In constructor ‘oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)’: include/oxli/assembler.hh:158:16: warning: ‘oxli::JunctionCountAssembler::_ksize’ will be initialized after [-Wreorder] 158 | WordLength _ksize; | ^~~~~~ include/oxli/assembler.hh:153:15: warning: ‘oxli::Traverser oxli::JunctionCountAssembler::traverser’ [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh:153:15: warning: ‘oxli::JunctionCountAssembler::traverser’ will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ include/oxli/assembler.hh:151:21: warning: ‘oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm’ [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hashgraph.cc -o build/temp.linux-arm64-3.10/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hashtable.cc -o build/temp.linux-arm64-3.10/src/oxli/hashtable.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hashtable.cc:512:1: required from here src/oxli/hashtable.cc:103:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 103 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hashtable.cc:529:1: required from here src/oxli/hashtable.cc:133:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 133 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hllcounter.cc -o build/temp.linux-arm64-3.10/src/oxli/hllcounter.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hllcounter.cc: In instantiation of ‘void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hllcounter.cc:524:1: required from here src/oxli/hllcounter.cc:428:40: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 428 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/kmer_filters.cc -o build/temp.linux-arm64-3.10/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/kmer_hash.cc -o build/temp.linux-arm64-3.10/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/labelhash.cc -o build/temp.linux-arm64-3.10/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/read_aligner.cc -o build/temp.linux-arm64-3.10/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/read_parsers.cc -o build/temp.linux-arm64-3.10/src/oxli/read_parsers.o -O3 -std=c++11 -pedantic -fopenmp In file included from third-party/seqan/core/include/seqan/basic.h:62, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, from third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/modifier.h:66, from third-party/seqan/core/include/seqan/file.h:48, from third-party/seqan/core/include/seqan/stream.h:70, from third-party/seqan/core/include/seqan/seq_io.h:45: third-party/seqan/core/include/seqan/modifier/modifier_functors.h:68:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 68 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from src/oxli/read_parsers.cc:38: /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:91:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 91 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:115:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 115 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:169:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 169 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:178:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 178 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:188:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 188 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:198:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 198 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:208:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 208 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:217:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 217 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:229:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/file.h:117: third-party/seqan/core/include/seqan/file/string_external.h:1316:51: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1316 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/graph_algorithms.h:46, from third-party/seqan/core/include/seqan/graph_align.h:47, from third-party/seqan/core/include/seqan/align.h:54, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83: third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:340:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 340 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/graph_algorithms.h:47: third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm.h:643:23: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 643 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:79: third-party/seqan/core/include/seqan/align/gap_anchor.h:246:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/align/gap_anchor.h:256:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:116: third-party/seqan/core/include/seqan/align/dp_cell_affine.h: In member function ‘seqan::DPCell_ >& seqan::DPCell_ >::operator=(const seqan::DPCell_ >&)’: third-party/seqan/core/include/seqan/align/dp_cell_affine.h:84:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 84 | if (this != &other) | ^~ third-party/seqan/core/include/seqan/align/dp_cell_affine.h:86:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 86 | _horizontalScore = other._horizontalScore; | ^~~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:166: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)’: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from third-party/seqan/core/include/seqan/align.h:174: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41: third-party/seqan/core/include/seqan/bam_io/bam_stream.h: At global scope: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:59: third-party/seqan/core/include/seqan/store/store_align.h:322:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 322 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:332:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 332 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:342:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 342 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:352:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:362:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:372:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61: third-party/seqan/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)’: third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1733 | if (alignQualityStoreLengthPre == 0u) | ^~ third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/storage.cc -o build/temp.linux-arm64-3.10/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/subset.cc -o build/temp.linux-arm64-3.10/src/oxli/subset.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/subset.cc: In member function ‘size_t oxli::SubsetPartition::output_partitioned_file(const std::string&, const std::string&, bool, oxli::CallbackFn, void*)’: src/oxli/subset.cc:136:24: warning: unused variable ‘ksize’ [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/traversal.cc -o build/temp.linux-arm64-3.10/src/oxli/traversal.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:202:5: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:203:5: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-arm64-3.10/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-arm64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-arm64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-arm64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-arm64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-arm64-3.10/src/khmer/_cpy_utils.o build/temp.linux-arm64-3.10/src/oxli/alphabets.o build/temp.linux-arm64-3.10/src/oxli/assembler.o build/temp.linux-arm64-3.10/src/oxli/hashgraph.o build/temp.linux-arm64-3.10/src/oxli/hashtable.o build/temp.linux-arm64-3.10/src/oxli/hllcounter.o build/temp.linux-arm64-3.10/src/oxli/kmer_filters.o build/temp.linux-arm64-3.10/src/oxli/kmer_hash.o build/temp.linux-arm64-3.10/src/oxli/labelhash.o build/temp.linux-arm64-3.10/src/oxli/read_aligner.o build/temp.linux-arm64-3.10/src/oxli/read_parsers.o build/temp.linux-arm64-3.10/src/oxli/storage.o build/temp.linux-arm64-3.10/src/oxli/subset.o build/temp.linux-arm64-3.10/src/oxli/traversal.o build/temp.linux-arm64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_khmer.cpython-310-aarch64-linux-gnu.so -fopenmp running build_scripts running install_lib creating /<>/debian/khmer creating /<>/debian/khmer/usr creating /<>/debian/khmer/usr/lib creating /<>/debian/khmer/usr/lib/python3.10 creating /<>/debian/khmer/usr/lib/python3.10/dist-packages creating /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/trimming.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/khmer_args.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/kfile.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer creating /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/__pycache__/utils.cpython-310.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/__pycache__/__init__.cpython-310.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/__pycache__/_version.cpython-310.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/__pycache__/kfile.cpython-310.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/__pycache__/khmer_args.cpython-310.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/__pycache__/khmer_logger.cpython-310.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/__pycache__/trimming.cpython-310.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/__pycache__/thread_utils.cpython-310.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/__pycache__ creating /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.cpp -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/utils.cpython-310-aarch64-linux-gnu.so -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.cpython-310-aarch64-linux-gnu.so -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/graphs.pxd -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/parsing.pxd -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hllcounter.pxd -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/traversal.pxd -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.pyx -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.cpp -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/utils.pxd -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/parsing.pyx -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/parsing.cpp -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.pyx -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/graphs.pyx -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/utils.cpp -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.pxd -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/utils.pyx -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/parsing.cpython-310-aarch64-linux-gnu.so -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli creating /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/__pycache__/__init__.cpython-310.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/oxli_types.pxd -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/__init__.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.cpython-310-aarch64-linux-gnu.so -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.pxd -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/graphs.cpython-310-aarch64-linux-gnu.so -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/graphs.cpp -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/khmer_logger.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_khmer.cpython-310-aarch64-linux-gnu.so -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer creating /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_cython_parsing.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_banding.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_script_arguments.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_labelhash.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_cython_assembly.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_functions.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_lump.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests creating /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-3.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-multi.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/badversion-k12.ct -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-fastq-reads.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-sweep-contigs.fp -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/readaligner-default.json -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken.fq.badright -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/all-A.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.malformat.fq.2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/old-style-format-w-comments.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/100-reads.fq.gz -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/filter-test-B.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fa.gz -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken2.fq.1 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.bz2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-fastq-n-reads.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken4.fq.1 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-sweep-reads.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fq.bz2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/badversion-k32.stoptags -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/filter-test-A.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/real-partition-small.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-large.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/goodversion-k12.ht -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/readaligner-k12.json -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken3.fq.1 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/casava_18-pe.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/dn-test-none-paired.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-filter-abund-Ns.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/fakelump.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken2.fq.2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed-2.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/valid-read-testing.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-graph5.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-graph.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-empty.fa.bz2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken.fq.2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-short.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fa.bz2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fa.part -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.gz -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-output-partitions.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/unclean-reads.fastq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-slash1.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/empty-file.gz -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-fastq-reads.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/badversion-k32.tagset -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-labels.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/dn-test-all-paired-all-keep.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fa.se -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fq.pe -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-overlap1.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-graph2.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-overlap2.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken4.fq.2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired_one.base.dif.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/real-partition-tiny.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/goodversion-k32.stoptags -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-paired.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/empty-file.bz2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/empty-file -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken3.fq.2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/README.rst -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fq.2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/multi-output.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.paired.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-transcript.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed-witherror.fa.pe -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/truncated.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/100-reads.fq.bz2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/normC20k20.ct -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-X2.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/single-read.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fa.1 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/bogus.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/goodversion-k32.tagset -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/badversion-k12.ht -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fq.1 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.malformat.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-error-reads.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/simple-genome.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fq.se -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken.fq.paired_bad -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-paired.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-reads.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-31-c.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-slash1.fq.1 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/single-read.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.odd.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/combine_parts_1.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fq.gz -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-sweep-reads.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken.fq.badleft -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/dn-test-some-paired-all-keep.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed-broken.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/banding-reads.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.gz -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-reads.fq.gz -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.paired2.fq -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.even.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/fakelump.fa.stoptags.txt -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken.fq.1 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-impaired.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-empty.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.bz2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fa.2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/goodversion-k12.ht.gz -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-slash1.fq.2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/simple-genome-reads.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fa.pe -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/biglump-random-20-a.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-b.fa -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-reads.fq.bz2 -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/graph_features.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_nibblestorage.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_hashset.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_sandbox_scripts.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_nodegraph.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_version.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_read_aligner.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_countgraph.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_read_handling.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_threaded_sequence_processor.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/.gitignore -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests creating /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_script_output.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_nibblestorage.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_labelhash.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_oxli_functions.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_sandbox_scripts.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_tabletype.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_read_handling.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/__init__.cpython-310.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_sequence_validation.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_version.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_lump.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_hll.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/khmer_tst_utils.cpython-310.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_graph.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_script_arguments.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_subset_graph.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_countgraph.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_filter_abund.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_counttable.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_counting_single.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_cython_parsing.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_read_aligner.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_normalize_by_median.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/graph_features.cpython-310.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_read_parsers.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_functions.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_cython_assembly.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_streaming_io.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_hashset.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_banding.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_cpython_hierarchy.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_nodegraph.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_scripts.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__pycache__/test_threaded_sequence_processor.cpython-310-pytest-7.1.2.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_hll.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_counttable.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_normalize_by_median.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_scripts.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_subset_graph.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__init__.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/khmer_tst_utils.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_cpython_hierarchy.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_sequence_validation.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_filter_abund.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_counting_single.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_script_output.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_read_parsers.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_tabletype.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_oxli_functions.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_streaming_io.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_graph.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_version.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/__init__.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/utils.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/thread_utils.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer creating /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/oxli/build_graph.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/oxli/functions.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli creating /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/oxli/__pycache__/__init__.cpython-310.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/oxli/__pycache__/partition.cpython-310.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/oxli/__pycache__/functions.cpython-310.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/oxli/__pycache__/build_graph.cpython-310.pyc -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli/__pycache__ copying /<>/.pybuild/cpython3_3.10_khmer/build/oxli/__init__.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/oxli/partition.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/trimming.py to trimming.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/khmer_args.py to khmer_args.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/kfile.py to kfile.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/khmer_logger.py to khmer_logger.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_cython_parsing.py to test_cython_parsing.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_banding.py to test_banding.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_script_arguments.py to test_script_arguments.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_labelhash.py to test_labelhash.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_cython_assembly.py to test_cython_assembly.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_functions.py to test_functions.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_lump.py to test_lump.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/graph_features.py to graph_features.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_nibblestorage.py to test_nibblestorage.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_hashset.py to test_hashset.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_sandbox_scripts.py to test_sandbox_scripts.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_nodegraph.py to test_nodegraph.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_version.py to test_version.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_read_aligner.py to test_read_aligner.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_countgraph.py to test_countgraph.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_read_handling.py to test_read_handling.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_threaded_sequence_processor.py to test_threaded_sequence_processor.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_hll.py to test_hll.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_counttable.py to test_counttable.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_normalize_by_median.py to test_normalize_by_median.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_scripts.py to test_scripts.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py to test_subset_graph.cpython-310.pyc /usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py:61: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py:82: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py:278: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py:476: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py:509: SyntaxWarning: "is" with a literal. Did you mean "=="? byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/khmer_tst_utils.py to khmer_tst_utils.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_cpython_hierarchy.py to test_cpython_hierarchy.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_sequence_validation.py to test_sequence_validation.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_filter_abund.py to test_filter_abund.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_counting_single.py to test_counting_single.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_script_output.py to test_script_output.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_read_parsers.py to test_read_parsers.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_tabletype.py to test_tabletype.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_oxli_functions.py to test_oxli_functions.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_streaming_io.py to test_streaming_io.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_graph.py to test_graph.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_version.py to _version.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/utils.py to utils.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/thread_utils.py to thread_utils.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli/build_graph.py to build_graph.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli/functions.py to functions.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/khmer/usr/lib/python3.10/dist-packages/oxli/partition.py to partition.cpython-310.pyc running install_egg_info Copying khmer.egg-info to /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer-2.1.2.egg-info Skipping SOURCES.txt running install_scripts creating /<>/debian/khmer/usr/lib/khmer creating /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/annotate-partitions.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/find-knots.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/load-into-counting.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/partition-graph.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/trim-low-abund.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/filter-stoptags.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/extract-long-sequences.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/normalize-by-median.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/readstats.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/make-initial-stoptags.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/unique-kmers.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/merge-partitions.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/filter-abund.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/load-graph.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/abundance-dist-single.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/extract-paired-reads.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/interleave-reads.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/do-partition.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/sample-reads-randomly.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/abundance-dist.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/extract-partitions.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/fastq-to-fasta.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/split-paired-reads.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/count-median.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/filter-abund-single.py -> /<>/debian/khmer/usr/lib/khmer/bin changing mode of /<>/debian/khmer/usr/lib/khmer/bin/annotate-partitions.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/find-knots.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/load-into-counting.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/partition-graph.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/trim-low-abund.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/filter-stoptags.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/extract-long-sequences.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/normalize-by-median.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/readstats.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/make-initial-stoptags.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/unique-kmers.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/merge-partitions.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/filter-abund.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/load-graph.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/abundance-dist-single.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/extract-paired-reads.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/interleave-reads.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/do-partition.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/sample-reads-randomly.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/abundance-dist.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/extract-partitions.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/fastq-to-fasta.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/split-paired-reads.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/count-median.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/filter-abund-single.py to 755 rm -f debian/khmer.debhelper.log debian/liboxli-dev.debhelper.log debian/liboxli1.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/<>' cd src/oxli && /usr/bin/make PREFIX=../debian/tmp install make[2]: Entering directory '/<>/src/oxli' rm -rf ../debian/tmp/include/oxli ../debian/tmp/include/khmer mkdir -p ../debian/tmp/lib ../debian/tmp/lib/pkgconfig ../debian/tmp/include/oxli cp -r ../../include/oxli/hashtable.hh ../../include/oxli/hashgraph.hh ../../include/oxli/hllcounter.hh ../../include/oxli/oxli_exception.hh ../../include/oxli/oxli.hh ../../include/oxli/kmer_hash.hh ../../include/oxli/labelhash.hh ../../include/oxli/traversal.hh ../../include/oxli/read_aligner.hh ../../include/oxli/read_parsers.hh ../../include/oxli/subset.hh ../../include/oxli/kmer_filters.hh ../../include/oxli/assembler.hh ../../include/oxli/alphabets.hh ../../include/oxli/storage.hh \ ../../third-party/smhasher/MurmurHash3.h \ ../debian/tmp/include/oxli/ cp oxli.pc ../debian/tmp/lib/pkgconfig/ cp liboxli.so.1 liboxli.a ../debian/tmp/lib/ ln -sf ../debian/tmp/lib/liboxli.so.1 ../debian/tmp/lib/liboxli.so make[2]: Leaving directory '/<>/src/oxli' dh_install install -d debian/.debhelper/generated/khmer-common install -d debian/khmer//usr/share/metainfo/ cp --reflink=auto -a ./debian/khmer.metainfo.xml debian/khmer//usr/share/metainfo// install -d debian/khmer/usr/bin/ cp --reflink=auto -a ./debian/bin/khmer debian/khmer/usr/bin// install -d debian/.debhelper/generated/khmer install -d debian/liboxli1/usr/lib/aarch64-linux-gnu cp --reflink=auto -a ./src/oxli/liboxli.so.1 debian/liboxli1/usr/lib/aarch64-linux-gnu/ install -d debian/.debhelper/generated/liboxli1 install -d debian/liboxli-dev/usr/include/oxli cp --reflink=auto -a ./include/oxli/alphabets.hh ./include/oxli/assembler.hh ./include/oxli/hashgraph.hh ./include/oxli/hashtable.hh ./include/oxli/hllcounter.hh ./include/oxli/kmer_filters.hh ./include/oxli/kmer_hash.hh ./include/oxli/labelhash.hh ./include/oxli/oxli.hh ./include/oxli/oxli_exception.hh ./include/oxli/read_aligner.hh ./include/oxli/read_parsers.hh ./include/oxli/storage.hh ./include/oxli/subset.hh ./include/oxli/traversal.hh debian/liboxli-dev/usr/include/oxli/ install -d debian/liboxli-dev/usr/include/oxli/smhasher cp --reflink=auto -a ./third-party/smhasher/MurmurHash3.h debian/liboxli-dev/usr/include/oxli/smhasher/ install -d debian/liboxli-dev/usr/lib/aarch64-linux-gnu cp --reflink=auto -a ./src/oxli/liboxli.a ./src/oxli/liboxli.so debian/liboxli-dev/usr/lib/aarch64-linux-gnu/ install -d debian/liboxli-dev/usr/lib/aarch64-linux-gnu/pkgconfig cp --reflink=auto -a ./src/oxli/oxli.pc debian/liboxli-dev/usr/lib/aarch64-linux-gnu/pkgconfig/ install -d debian/.debhelper/generated/liboxli-dev find debian/khmer -name .gitignore -delete make[1]: Leaving directory '/<>' dh_installdocs -a -O--buildsystem=pybuild install -d debian/khmer/usr/share/doc/khmer install -p -m0644 debian/copyright debian/khmer/usr/share/doc/khmer/copyright install -d debian/liboxli1/usr/share/doc/liboxli1 install -p -m0644 debian/copyright debian/liboxli1/usr/share/doc/liboxli1/copyright install -d debian/liboxli-dev/usr/share/doc/liboxli-dev install -p -m0644 debian/copyright debian/liboxli-dev/usr/share/doc/liboxli-dev/copyright rm -f debian/khmer.debhelper.log debian/liboxli-dev.debhelper.log debian/liboxli1.debhelper.log debian/rules override_dh_sphinxdoc make[1]: Entering directory '/<>' find: ‘debian/khmer-common’: No such file or directory dh_sphinxdoc dh_sphinxdoc: warning: Sphinx documentation not found rdfind -makesymlinks true -followsymlinks true\ /usr/lib/python3/dist-packages/guzzle_sphinx_theme \ Now scanning "/usr/lib/python3/dist-packages/guzzle_sphinx_theme", found 116 files. Now have 116 files in total. Removed 14 files due to nonunique device and inode. Total size is 5331022 bytes or 5 MiB Removed 100 files due to unique sizes from list. 2 files left. Now eliminating candidates based on first bytes: removed 2 files from list. 0 files left. Now eliminating candidates based on last bytes: removed 0 files from list. 0 files left. Now eliminating candidates based on sha1 checksum: removed 0 files from list. 0 files left. It seems like you have 0 files that are not unique Totally, 0 B can be reduced. Now making results file results.txt Now making symbolic links. creating Making 0 links. if [ -f debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt ]; then \ rm debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt && \ cd debian/khmer-common/usr/share/doc/khmer-common/html/_sources/ && \ ln -s ../../CITATION citations.rst.txt; fi make[1]: Leaving directory '/<>' dh_installchangelogs -a -O--buildsystem=pybuild install -p -m0644 debian/changelog debian/liboxli-dev/usr/share/doc/liboxli-dev/changelog.Debian install -p -m0644 debian/changelog debian/khmer/usr/share/doc/khmer/changelog.Debian install -p -m0644 debian/changelog debian/liboxli1/usr/share/doc/liboxli1/changelog.Debian dh_installman -a -O--buildsystem=pybuild install -d debian/khmer/usr/share/man/man1/ install -p -m0644 ./debian/khmer.1 debian/khmer/usr/share/man/man1/khmer.1 man-recode --to-code UTF-8 --suffix .dh-new debian/khmer/usr/share/man/man1/khmer.1 mv debian/khmer/usr/share/man/man1/khmer.1.dh-new debian/khmer/usr/share/man/man1/khmer.1 chmod 0644 -- debian/khmer/usr/share/man/man1/khmer.1 dh_python3 -a -O--buildsystem=pybuild D: dh_python3 dh_python3:175: version: 5.20220819 D: dh_python3 dh_python3:176: argv: ['/usr/bin/dh_python3', '-a', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:177: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=True, package=None, no_package=None, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=['--buildsystem=pybuild']) D: dh_python3 dh_python3:178: supported Python versions: 3.10 (default=3.10) D: dh_python3 debhelper:164: skipping package liboxli1 (missing ${python3:Depends} in Depends/Recommends) D: dh_python3 debhelper:164: skipping package liboxli-dev (missing ${python3:Depends} in Depends/Recommends) D: dh_python3 debhelper:172: source=khmer, binary packages=['khmer'] D: dh_python3 dh_python3:196: processing package khmer... D: dh_python3 fs:52: moving files from debian/khmer/usr/lib/python3.10/dist-packages to debian/khmer/usr/lib/python3/dist-packages/ D: dh_python3 tools:102: fix_shebang (debian/khmer/usr/bin/khmer): doesn't look like a shebang: #!/bin/sh D: dh_python3 fs:399: package khmer details = {'requires.txt': {'debian/khmer/usr/lib/python3/dist-packages/khmer-2.1.2.egg-info/requires.txt'}, 'egg-info': set(), 'dist-info': set(), 'nsp.txt': set(), 'shebangs': set(), 'public_vers': {Version('3')}, 'private_dirs': {'/usr/lib/khmer': {'shebangs': {/usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3}, 'compile': True}}, 'compile': True, 'ext_vers': {Version('3.10')}, 'ext_no_version': set()} D: dh_python3 depends:117: generating dependencies for package khmer D: dh_python3 pydist:172: trying to find dependency for Cython>=0.25.2 (python=None) D: dh_python3 pydist:172: trying to find dependency for screed>=1.0 (python=None) D: dh_python3 pydist:172: trying to find dependency for argparse>=1.2.1 (python=None) D: dh_python3 depends:281: D={'python3:any', 'python3 (>= 3.10~)', 'python3 (<< 3.11)', 'python3-screed', 'cython3', 'python3 (>= 3.2) | python3 (<< 2.6) | python3 (>> 2.7)'}; R=[]; S=[]; E=[], B=[]; RT=[('/usr/lib/khmer', '')] dh_installsystemduser -a -O--buildsystem=pybuild dh_lintian -a -O--buildsystem=pybuild install -d debian/khmer/usr/share/lintian/overrides install -p -m0644 debian/khmer.lintian-overrides debian/khmer/usr/share/lintian/overrides/khmer install -d debian/liboxli1/usr/share/lintian/overrides install -p -m0644 debian/liboxli1.lintian-overrides debian/liboxli1/usr/share/lintian/overrides/liboxli1 dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild rm -f debian/liboxli-dev/usr/lib/aarch64-linux-gnu/liboxli.so ln -s liboxli.so.1 debian/liboxli-dev/usr/lib/aarch64-linux-gnu/liboxli.so dh_strip_nondeterminism -a -O--buildsystem=pybuild Using 1661162028 as canonical time Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fa.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/test-abund-read-2.fa.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/empty-file.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fq.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.truncated.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/test-reads.fq.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/goodversion-k12.ht.gz using File::StripNondeterminism::handlers::gzip dh_compress -a -O--buildsystem=pybuild cd debian/khmer cd debian/liboxli1 cd debian/liboxli-dev chmod a-x usr/share/doc/liboxli1/changelog.Debian chmod a-x usr/share/doc/khmer/changelog.Debian usr/share/man/man1/khmer.1 chmod a-x usr/share/doc/liboxli-dev/changelog.Debian gzip -9nf usr/share/doc/liboxli1/changelog.Debian gzip -9nf usr/share/doc/khmer/changelog.Debian usr/share/man/man1/khmer.1 gzip -9nf usr/share/doc/liboxli-dev/changelog.Debian cd '/<>' cd '/<>' cd '/<>' dh_fixperms -a -O--buildsystem=pybuild find debian/khmer ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/liboxli1 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/liboxli-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/liboxli1/usr/share/doc -type f -a -true -a ! -regex 'debian/liboxli1/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/liboxli-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/khmer/usr/share/doc -type f -a -true -a ! -regex 'debian/khmer/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli1/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/liboxli-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/khmer/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/liboxli1/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/khmer/usr/share/man debian/khmer/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli1 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/khmer -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli1/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/liboxli-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/khmer/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/khmer/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dwz -- debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 install -d debian/khmer/usr/lib/debug/.dwz/aarch64-linux-gnu dwz -mdebian/khmer/usr/lib/debug/.dwz/aarch64-linux-gnu/khmer.debug -M/usr/lib/debug/.dwz/aarch64-linux-gnu/khmer.debug -- debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-aarch64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-aarch64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-aarch64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-aarch64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-aarch64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-aarch64-linux-gnu.so objcopy --compress-debug-sections debian/khmer/usr/lib/debug/.dwz/aarch64-linux-gnu/khmer.debug dh_strip -a -O--buildsystem=pybuild strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives -R .gnu.lto_\* -R .gnu.debuglto_\* -N __gnu_lto_slim -N __gnu_lto_v1 debian/liboxli-dev/usr/lib/aarch64-linux-gnu/liboxli.a debugedit --build-id --build-id-seed=liboxli1/2.1.2\+dfsg-11 debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 debugedit --build-id --build-id-seed=khmer/2.1.2\+dfsg-11 debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-aarch64-linux-gnu.so debugedit: debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-aarch64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 f52d490549e9d447df536b42dd4b1fe86de7076c install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/f5 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-aarch64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/f5/2d490549e9d447df536b42dd4b1fe86de7076c.debug readelf -W --section-headers debian/liboxli-dev/usr/lib/aarch64-linux-gnu/liboxli.a | sed -n '/^ *\[[ 0-9]*]/s/ *\[[ 0-9]*\] *//p' | awk 'BEGIN {rv=1} /^NULL/ {next} $1 ~ /^.(text|data|(preinit|init|fini)_array$)/ {if ($5 !~ /^0+$/) rv=0} END { exit rv}' cf26910945c3af7ba154d12d182a13c4f4b80213 install -d debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/cf objcopy --only-keep-debug --compress-debug-sections debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/cf/26910945c3af7ba154d12d182a13c4f4b80213.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/f5/2d490549e9d447df536b42dd4b1fe86de7076c.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/CySULHOcNc/stripOwoWXN debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-aarch64-linux-gnu.so chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-aarch64-linux-gnu.so /tmp/CySULHOcNc/stripOwoWXN cat '/tmp/CySULHOcNc/stripOwoWXN' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-aarch64-linux-gnu.so' chmod --reference /tmp/CySULHOcNc/stripOwoWXN debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/f5/2d490549e9d447df536b42dd4b1fe86de7076c.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-aarch64-linux-gnu.so /tmp/CySULHOcNc/objcopyoxGVC9 chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-aarch64-linux-gnu.so /tmp/CySULHOcNc/objcopyoxGVC9 cat '/tmp/CySULHOcNc/objcopyoxGVC9' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-aarch64-linux-gnu.so' chmod --reference /tmp/CySULHOcNc/objcopyoxGVC9 debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-aarch64-linux-gnu.so chmod 0644 -- debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/cf/26910945c3af7ba154d12d182a13c4f4b80213.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/UDMwIvBXsW/striphvMPmL debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 debugedit --build-id --build-id-seed=khmer/2.1.2\+dfsg-11 debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-aarch64-linux-gnu.so chmod --reference debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 /tmp/UDMwIvBXsW/striphvMPmL cat '/tmp/UDMwIvBXsW/striphvMPmL' > 'debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1' debugedit: debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-aarch64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 chmod --reference /tmp/UDMwIvBXsW/striphvMPmL debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 objcopy --add-gnu-debuglink debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/cf/26910945c3af7ba154d12d182a13c4f4b80213.debug debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 /tmp/UDMwIvBXsW/objcopypJC0jM bbb8237911ddd057cb3d83f9ea842cc6d31b69f9 chmod --reference debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 /tmp/UDMwIvBXsW/objcopypJC0jM cat '/tmp/UDMwIvBXsW/objcopypJC0jM' > 'debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1' install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/bb objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-aarch64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/bb/b8237911ddd057cb3d83f9ea842cc6d31b69f9.debug chmod --reference /tmp/UDMwIvBXsW/objcopypJC0jM debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 install -d debian/.debhelper/liboxli1/dbgsym-root/usr/share/doc ln -s liboxli1 debian/.debhelper/liboxli1/dbgsym-root/usr/share/doc/liboxli1-dbgsym chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/bb/b8237911ddd057cb3d83f9ea842cc6d31b69f9.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/CySULHOcNc/stripfjmnyX debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-aarch64-linux-gnu.so chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-aarch64-linux-gnu.so /tmp/CySULHOcNc/stripfjmnyX cat '/tmp/CySULHOcNc/stripfjmnyX' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-aarch64-linux-gnu.so' chmod --reference /tmp/CySULHOcNc/stripfjmnyX debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/bb/b8237911ddd057cb3d83f9ea842cc6d31b69f9.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-aarch64-linux-gnu.so /tmp/CySULHOcNc/objcopyNV5Lj7 chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-aarch64-linux-gnu.so /tmp/CySULHOcNc/objcopyNV5Lj7 cat '/tmp/CySULHOcNc/objcopyNV5Lj7' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-aarch64-linux-gnu.so' chmod --reference /tmp/CySULHOcNc/objcopyNV5Lj7 debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-aarch64-linux-gnu.so debugedit --build-id --build-id-seed=khmer/2.1.2\+dfsg-11 debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-aarch64-linux-gnu.so debugedit: debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-aarch64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 4c0f8302ed0143b94b56af09634066fedf3667da install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/4c objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-aarch64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/4c/0f8302ed0143b94b56af09634066fedf3667da.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/4c/0f8302ed0143b94b56af09634066fedf3667da.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/CySULHOcNc/stripDUmp2A debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-aarch64-linux-gnu.so chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-aarch64-linux-gnu.so /tmp/CySULHOcNc/stripDUmp2A cat '/tmp/CySULHOcNc/stripDUmp2A' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-aarch64-linux-gnu.so' chmod --reference /tmp/CySULHOcNc/stripDUmp2A debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/4c/0f8302ed0143b94b56af09634066fedf3667da.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-aarch64-linux-gnu.so /tmp/CySULHOcNc/objcopymS4OgT chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-aarch64-linux-gnu.so /tmp/CySULHOcNc/objcopymS4OgT cat '/tmp/CySULHOcNc/objcopymS4OgT' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-aarch64-linux-gnu.so' chmod --reference /tmp/CySULHOcNc/objcopymS4OgT debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-aarch64-linux-gnu.so debugedit --build-id --build-id-seed=khmer/2.1.2\+dfsg-11 debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-aarch64-linux-gnu.so debugedit: debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-aarch64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 f382f5a755980136b7b947dd0a125461231dafe6 install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/f3 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-aarch64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/f3/82f5a755980136b7b947dd0a125461231dafe6.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/f3/82f5a755980136b7b947dd0a125461231dafe6.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/CySULHOcNc/stripGQMpMb debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-aarch64-linux-gnu.so chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-aarch64-linux-gnu.so /tmp/CySULHOcNc/stripGQMpMb cat '/tmp/CySULHOcNc/stripGQMpMb' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-aarch64-linux-gnu.so' chmod --reference /tmp/CySULHOcNc/stripGQMpMb debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/f3/82f5a755980136b7b947dd0a125461231dafe6.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-aarch64-linux-gnu.so /tmp/CySULHOcNc/objcopytRqRYn chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-aarch64-linux-gnu.so /tmp/CySULHOcNc/objcopytRqRYn cat '/tmp/CySULHOcNc/objcopytRqRYn' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-aarch64-linux-gnu.so' chmod --reference /tmp/CySULHOcNc/objcopytRqRYn debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-aarch64-linux-gnu.so debugedit --build-id --build-id-seed=khmer/2.1.2\+dfsg-11 debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-aarch64-linux-gnu.so debugedit: debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-aarch64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 7cdaede61a558639264f59e6ea51ec55deab4cf1 install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/7c objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-aarch64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/7c/daede61a558639264f59e6ea51ec55deab4cf1.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/7c/daede61a558639264f59e6ea51ec55deab4cf1.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/CySULHOcNc/stripvywMkm debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-aarch64-linux-gnu.so chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-aarch64-linux-gnu.so /tmp/CySULHOcNc/stripvywMkm cat '/tmp/CySULHOcNc/stripvywMkm' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-aarch64-linux-gnu.so' chmod --reference /tmp/CySULHOcNc/stripvywMkm debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/7c/daede61a558639264f59e6ea51ec55deab4cf1.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-aarch64-linux-gnu.so /tmp/CySULHOcNc/objcopyjg00TT chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-aarch64-linux-gnu.so /tmp/CySULHOcNc/objcopyjg00TT cat '/tmp/CySULHOcNc/objcopyjg00TT' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-aarch64-linux-gnu.so' chmod --reference /tmp/CySULHOcNc/objcopyjg00TT debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-aarch64-linux-gnu.so debugedit --build-id --build-id-seed=khmer/2.1.2\+dfsg-11 debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-aarch64-linux-gnu.so debugedit: debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-aarch64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 1dc7ad10d1a50ef9dc427f9e244bceffcbbe7ded install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/1d objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-aarch64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/1d/c7ad10d1a50ef9dc427f9e244bceffcbbe7ded.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/1d/c7ad10d1a50ef9dc427f9e244bceffcbbe7ded.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/CySULHOcNc/stripmxSYV0 debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-aarch64-linux-gnu.so chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-aarch64-linux-gnu.so /tmp/CySULHOcNc/stripmxSYV0 cat '/tmp/CySULHOcNc/stripmxSYV0' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-aarch64-linux-gnu.so' chmod --reference /tmp/CySULHOcNc/stripmxSYV0 debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/1d/c7ad10d1a50ef9dc427f9e244bceffcbbe7ded.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-aarch64-linux-gnu.so /tmp/CySULHOcNc/objcopymJmAjp chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-aarch64-linux-gnu.so /tmp/CySULHOcNc/objcopymJmAjp cat '/tmp/CySULHOcNc/objcopymJmAjp' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-aarch64-linux-gnu.so' chmod --reference /tmp/CySULHOcNc/objcopymJmAjp debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-aarch64-linux-gnu.so install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/khmer/usr/lib/debug/.dwz/aarch64-linux-gnu debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/khmer/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/khmer/usr/lib/debug install -d debian/.debhelper/khmer/dbgsym-root/usr/share/doc ln -s khmer debian/.debhelper/khmer/dbgsym-root/usr/share/doc/khmer-dbgsym dh_makeshlibs -a -O--buildsystem=pybuild rm -f debian/khmer/DEBIAN/shlibs rm -f debian/liboxli1/DEBIAN/shlibs install -d debian/liboxli1/DEBIAN echo "liboxli 1 liboxli1 (>= 2.1.2+dfsg)" >> debian/liboxli1/DEBIAN/shlibs chmod 0644 -- debian/liboxli1/DEBIAN/shlibs mv debian/.debhelper/generated/liboxli1/triggers.new debian/.debhelper/generated/liboxli1/triggers rm -f debian/liboxli-dev/DEBIAN/shlibs dh_shlibdeps -a -O--buildsystem=pybuild dpkg-shlibdeps -Tdebian/liboxli1.substvars debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 install -d debian/khmer/DEBIAN dpkg-shlibdeps -Tdebian/khmer.substvars debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-aarch64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-aarch64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-aarch64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-aarch64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-aarch64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-aarch64-linux-gnu.so dpkg-shlibdeps: warning: symbol gzdirect used by debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzread used by debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol BZ2_bzRead used by debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol BZ2_bzReadClose used by debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzerror used by debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol inflateEnd used by debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol deflateInit2_ used by debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzopen64 used by debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol inflate used by debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzeof used by debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: 13 other similar warnings have been skipped (use -v to see them all) dh_installdeb -a -O--buildsystem=pybuild printf '#!/bin/sh\nset -e\n' > debian/khmer/DEBIAN/postinst cat debian/khmer.postinst.debhelper >> debian/khmer/DEBIAN/postinst chmod 0755 -- debian/khmer/DEBIAN/postinst printf '#!/bin/sh\nset -e\n' > debian/khmer/DEBIAN/prerm cat debian/khmer.prerm.debhelper >> debian/khmer/DEBIAN/prerm chmod 0755 -- debian/khmer/DEBIAN/prerm install -p -m0644 debian/.debhelper/generated/liboxli1/triggers debian/liboxli1/DEBIAN/triggers install -d debian/liboxli-dev/DEBIAN dh_gencontrol -a -O--buildsystem=pybuild echo misc:Depends= >> debian/liboxli-dev.substvars echo misc:Pre-Depends= >> debian/liboxli-dev.substvars dpkg-gencontrol -pliboxli-dev -ldebian/changelog -Tdebian/liboxli-dev.substvars -Pdebian/liboxli-dev echo misc:Depends= >> debian/khmer.substvars echo misc:Pre-Depends= >> debian/khmer.substvars install -d debian/.debhelper/khmer/dbgsym-root/DEBIAN dpkg-gencontrol -pkhmer -ldebian/changelog -Tdebian/khmer.substvars -Pdebian/.debhelper/khmer/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=khmer-dbgsym "-DDepends=khmer (= \${binary:Version})" "-DDescription=debug symbols for khmer" "-DBuild-Ids=1dc7ad10d1a50ef9dc427f9e244bceffcbbe7ded 4c0f8302ed0143b94b56af09634066fedf3667da 7cdaede61a558639264f59e6ea51ec55deab4cf1 bbb8237911ddd057cb3d83f9ea842cc6d31b69f9 f382f5a755980136b7b947dd0a125461231dafe6 f52d490549e9d447df536b42dd4b1fe86de7076c" -DSection=debug -DPackage-Type=ddeb -UMulti-Arch -UReplaces -UBreaks echo misc:Depends= >> debian/liboxli1.substvars echo misc:Pre-Depends= >> debian/liboxli1.substvars install -d debian/.debhelper/liboxli1/dbgsym-root/DEBIAN dpkg-gencontrol -pliboxli1 -ldebian/changelog -Tdebian/liboxli1.substvars -Pdebian/.debhelper/liboxli1/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=liboxli1-dbgsym "-DDepends=liboxli1 (= \${binary:Version})" "-DDescription=debug symbols for liboxli1" -DBuild-Ids=cf26910945c3af7ba154d12d182a13c4f4b80213 -DSection=debug -DPackage-Type=ddeb -UReplaces -UBreaks chmod 0644 -- debian/liboxli-dev/DEBIAN/control chmod 0644 -- debian/.debhelper/liboxli1/dbgsym-root/DEBIAN/control dpkg-gencontrol -pliboxli1 -ldebian/changelog -Tdebian/liboxli1.substvars -Pdebian/liboxli1 chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/DEBIAN/control dpkg-gencontrol -pkhmer -ldebian/changelog -Tdebian/khmer.substvars -Pdebian/khmer chmod 0644 -- debian/liboxli1/DEBIAN/control chmod 0644 -- debian/khmer/DEBIAN/control dh_md5sums -a -O--buildsystem=pybuild cd debian/liboxli1 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/khmer >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/liboxli-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/liboxli1/DEBIAN/md5sums cd debian/.debhelper/liboxli1/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/liboxli-dev/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/liboxli1/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/khmer/DEBIAN/md5sums cd debian/.debhelper/khmer/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/DEBIAN/md5sums dh_builddeb -a -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/khmer .. dpkg-deb --root-owner-group --build debian/liboxli1 .. dpkg-deb --root-owner-group --build debian/liboxli-dev .. INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing liboxli-dev (in debian/liboxli-dev); do_strip: , oemstrip: pkgstriptranslations: processing liboxli1 (in debian/liboxli1); do_strip: , oemstrip: pkgstriptranslations: processing khmer (in debian/khmer); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/liboxli-dev/DEBIAN/control, package liboxli-dev, directory debian/liboxli-dev INFO: pkgstripfiles: waiting for lock (liboxli-dev) ... pkgstripfiles: processing control file: debian/khmer/DEBIAN/control, package khmer, directory debian/khmer INFO: pkgstripfiles: waiting for lock (liboxli-dev) ... pkgstripfiles: Truncating usr/share/doc/khmer/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package khmer ... pkgstripfiles: No PNG files. dpkg-deb: building package 'khmer' in '../khmer_2.1.2+dfsg-11_arm64.deb'. INFO: pkgstripfiles: waiting for lock (liboxli-dev) ... pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " INFO: pkgstripfiles: waiting for lock (liboxli-dev) ... INFO: pkgstripfiles: waiting for lock (liboxli-dev) ... pkgstripfiles: processing control file: debian/liboxli1/DEBIAN/control, package liboxli1, directory debian/liboxli1 pkgstripfiles: Truncating usr/share/doc/liboxli1/changelog.Debian.gz to topmost ten records INFO: pkgstripfiles: waiting for lock (liboxli-dev) ... pkgstripfiles: Running PNG optimization (using 4 cpus) for package liboxli1 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'liboxli1' in '../liboxli1_2.1.2+dfsg-11_arm64.deb'. Searching for duplicated docs in dependency liboxli1... symlinking changelog.Debian.gz in liboxli-dev to file in liboxli1 pkgstripfiles: Running PNG optimization (using 4 cpus) for package liboxli-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'liboxli-dev' in '../liboxli-dev_2.1.2+dfsg-11_arm64.deb'. install -d debian/.debhelper/scratch-space/build-liboxli1 dpkg-deb --root-owner-group --build debian/.debhelper/liboxli1/dbgsym-root debian/.debhelper/scratch-space/build-liboxli1 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing liboxli1-dbgsym (in debian/.debhelper/liboxli1/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/liboxli1/dbgsym-root/DEBIAN/control, package liboxli1-dbgsym, directory debian/.debhelper/liboxli1/dbgsym-root dpkg-deb: building package 'liboxli1-dbgsym' in 'debian/.debhelper/scratch-space/build-liboxli1/liboxli1-dbgsym_2.1.2+dfsg-11_arm64.deb'. Renaming liboxli1-dbgsym_2.1.2+dfsg-11_arm64.deb to liboxli1-dbgsym_2.1.2+dfsg-11_arm64.ddeb mv debian/.debhelper/scratch-space/build-liboxli1/liboxli1-dbgsym_2.1.2\+dfsg-11_arm64.deb ../liboxli1-dbgsym_2.1.2\+dfsg-11_arm64.ddeb install -d debian/.debhelper/scratch-space/build-khmer dpkg-deb --root-owner-group --build debian/.debhelper/khmer/dbgsym-root debian/.debhelper/scratch-space/build-khmer INFO: pkgstriptranslations version 149 pkgstriptranslations: processing khmer-dbgsym (in debian/.debhelper/khmer/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/khmer/dbgsym-root/DEBIAN/control, package khmer-dbgsym, directory debian/.debhelper/khmer/dbgsym-root dpkg-deb: building package 'khmer-dbgsym' in 'debian/.debhelper/scratch-space/build-khmer/khmer-dbgsym_2.1.2+dfsg-11_arm64.deb'. Renaming khmer-dbgsym_2.1.2+dfsg-11_arm64.deb to khmer-dbgsym_2.1.2+dfsg-11_arm64.ddeb mv debian/.debhelper/scratch-space/build-khmer/khmer-dbgsym_2.1.2\+dfsg-11_arm64.deb ../khmer-dbgsym_2.1.2\+dfsg-11_arm64.ddeb dpkg-genbuildinfo --build=any -O../khmer_2.1.2+dfsg-11_arm64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../khmer_2.1.2+dfsg-11_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-08-23T00:53:15Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ khmer_2.1.2+dfsg-11_arm64.changes: ---------------------------------- Format: 1.8 Date: Mon, 22 Aug 2022 11:53:48 +0200 Source: khmer Binary: khmer liboxli-dev liboxli1 Built-For-Profiles: noudeb Architecture: arm64 Version: 2.1.2+dfsg-11 Distribution: kinetic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Michael R. Crusoe Description: khmer - in-memory DNA sequence kmer counting, filtering & graph traversal liboxli-dev - in-memory DNA sequence analysis dev library liboxli1 - in-memory DNA sequence analysis library from the khmer project Closes: 1008402 Changes: khmer (2.1.2+dfsg-11) unstable; urgency=medium . [ Stefano Rivera ] * Adapt to a change in Python3 Closes: #1008402 . [ Michael R. Crusoe ] * debian/patches: some header cleanups. * debian/patches/stringio-buffer.patch: another fix for recent Python versions. * Fix license mismatch in AppStream metadata * Standards-Version: 4.6.1 (routine-update) Checksums-Sha1: 4137491a2a14bca5c13e9c5eb37ffed29f1f39de 14902516 khmer-dbgsym_2.1.2+dfsg-11_arm64.ddeb 8973ba89dc408e281f483b0648a32eb66b9636e6 10251 khmer_2.1.2+dfsg-11_arm64.buildinfo 7f166559486c83dd962f3fd6ca62169d642cb293 6808468 khmer_2.1.2+dfsg-11_arm64.deb a1cff247fe9625cbde17daba8243d7ed74b845df 302524 liboxli-dev_2.1.2+dfsg-11_arm64.deb 30ebea9de72ec61be53e12a8d1d15a69593f070c 2151442 liboxli1-dbgsym_2.1.2+dfsg-11_arm64.ddeb 39c1deb0a9d89e7ffa63ff7ee0ef67dba4686a95 201952 liboxli1_2.1.2+dfsg-11_arm64.deb Checksums-Sha256: 8e7300bd3b783d98821885f165ed73a6111e6c7665b004ac358fa2474ee30d87 14902516 khmer-dbgsym_2.1.2+dfsg-11_arm64.ddeb 74a04354b1108ed558755cd5594011ef4e72044a2e5aa542ab2a0066ec679c3a 10251 khmer_2.1.2+dfsg-11_arm64.buildinfo 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Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: adduser (= 3.121ubuntu1), asciidoctor (= 2.0.16-2), autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-8), autotools-dev (= 20220109.1), base-files (= 12.2ubuntu2), base-passwd (= 3.6.0), bash (= 5.1-6ubuntu1), binutils (= 2.39-1ubuntu1), binutils-aarch64-linux-gnu (= 2.39-1ubuntu1), binutils-common (= 2.39-1ubuntu1), bsdextrautils (= 2.38-4ubuntu1), bsdutils (= 1:2.38-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), ca-certificates (= 20211016), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:12.1.0-3ubuntu1), cpp-11 (= 11.3.0-5ubuntu1), cpp-12 (= 12.1.0-8ubuntu2), cython3 (= 0.29.30-1ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-8ubuntu1), debconf (= 1.5.79ubuntu1), debhelper (= 13.9ubuntu1), debianutils (= 5.7-0.3), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-exec (= 0.27), dh-python (= 5.20220819), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 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2.38-4ubuntu1), util-linux-extra (= 2.38-4ubuntu1), xml-core (= 0.18+nmu1), xz-utils (= 5.2.5-2.1), zlib1g (= 1:1.2.11.dfsg-4.1ubuntu1), zlib1g-dev (= 1:1.2.11.dfsg-4.1ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1661162028" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ khmer_2.1.2+dfsg-11_arm64.deb ----------------------------- new Debian package, version 2.0. size 6808468 bytes: control archive=7060 bytes. 892 bytes, 16 lines control 22231 bytes, 230 lines md5sums 454 bytes, 19 lines * postinst #!/bin/sh 370 bytes, 12 lines * prerm #!/bin/sh Package: khmer Version: 2.1.2+dfsg-11 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 28969 Depends: khmer-common, python3 (<< 3.11), python3-screed, libbz2-1.0, libc6 (>= 2.32), libgcc-s1 (>= 3.3.1), libgomp1 (>= 4.9), libstdc++6 (>= 11), zlib1g (>= 1:1.2.3.4), cython3, python3 (>= 3.10~), python3:any Section: science Priority: optional Multi-Arch: foreign Homepage: https://khmer.readthedocs.org Description: in-memory DNA sequence kmer counting, filtering & graph traversal khmer is a library and suite of command line tools for working with DNA sequence. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform. khmer takes a k-mer-centric approach to sequence analysis, hence the name. drwxr-xr-x root/root 0 2022-08-22 09:53 ./ drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/ drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/bin/ -rwxr-xr-x root/root 569 2020-04-07 15:14 ./usr/bin/khmer drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/lib/ drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/lib/khmer/ drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/lib/khmer/bin/ -rwxr-xr-x root/root 8973 2022-08-22 09:53 ./usr/lib/khmer/bin/abundance-dist-single.py -rwxr-xr-x root/root 6877 2022-08-22 09:53 ./usr/lib/khmer/bin/abundance-dist.py -rwxr-xr-x root/root 4578 2022-08-22 09:53 ./usr/lib/khmer/bin/annotate-partitions.py -rwxr-xr-x root/root 5024 2022-08-22 09:53 ./usr/lib/khmer/bin/count-median.py -rwxr-xr-x root/root 8438 2022-08-22 09:53 ./usr/lib/khmer/bin/do-partition.py -rwxr-xr-x root/root 3716 2022-08-22 09:53 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drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/share/python3/runtime.d/ -rwxr-xr-x root/root 121 2022-08-22 09:53 ./usr/share/python3/runtime.d/khmer.rtupdate liboxli-dev_2.1.2+dfsg-11_arm64.deb ----------------------------------- new Debian package, version 2.0. size 302524 bytes: control archive=1246 bytes. 805 bytes, 19 lines control 1257 bytes, 19 lines md5sums Package: liboxli-dev Source: khmer Version: 2.1.2+dfsg-11 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1511 Depends: liboxli1 (= 2.1.2+dfsg-11), khmer-common Section: libdevel Priority: optional Multi-Arch: same Homepage: https://khmer.readthedocs.org Description: in-memory DNA sequence analysis dev library khmer is a library and suite of command line tools for working with DNA sequence. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform. khmer takes a k-mer-centric approach to sequence analysis, hence the name. . 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It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform. khmer takes a k-mer-centric approach to sequence analysis, hence the name. . This package contains the low-level C++ library. drwxr-xr-x root/root 0 2022-08-22 09:53 ./ drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/ drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/lib/ drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/lib/aarch64-linux-gnu/ -rw-r--r-- root/root 526368 2022-08-22 09:53 ./usr/lib/aarch64-linux-gnu/liboxli.so.1 drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/share/ drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/share/doc/liboxli1/ -rw-r--r-- root/root 1595 2022-08-22 09:53 ./usr/share/doc/liboxli1/changelog.Debian.gz -rw-r--r-- root/root 4466 2022-08-22 09:53 ./usr/share/doc/liboxli1/copyright drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/share/lintian/ drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 166 2020-04-07 15:14 ./usr/share/lintian/overrides/liboxli1 +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Type: any Build-Space: 594908 Build-Time: 9970 Distribution: kinetic-proposed Host Architecture: arm64 Install-Time: 333 Job: khmer_2.1.2+dfsg-11.dsc Machine Architecture: arm64 Package: khmer Package-Time: 10329 Source-Version: 2.1.2+dfsg-11 Space: 594908 Status: successful Version: 2.1.2+dfsg-11 -------------------------------------------------------------------------------- Finished at 2022-08-23T00:53:15Z Build needed 02:52:09, 594908k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=kinetic --arch=arm64 PACKAGEBUILD-24304739 Scanning for processes to kill in build PACKAGEBUILD-24304739