https://launchpad.net/ubuntu/+source/khmer/2.1.2+dfsg-11/+build/24304738 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-087 5.4.0-124-generic #140-Ubuntu SMP Thu Aug 4 02:23:37 UTC 2022 x86_64 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 17:18:33 ntpdate[1843]: adjust time server 10.131.248.1 offset 0.001361 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24304738 --image-type chroot /home/buildd/filecache-default/4d18961cd05542d5def75b14497015b674c37821 Creating target for build PACKAGEBUILD-24304738 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24304738 Starting target for build PACKAGEBUILD-24304738 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24304738 '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-24304738 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24304738 Updating target for build PACKAGEBUILD-24304738 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 amd64 Packages [1407 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/universe amd64 Packages [14.5 MB] Get:8 http://ftpmaster.internal/ubuntu kinetic/universe Translation-en [5796 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 Packages [196 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic-proposed/main Translation-en [52.8 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic-proposed/universe amd64 Packages [472 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic-proposed/universe Translation-en [220 kB] Fetched 23.7 MB in 3s (8213 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: 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-common binutils-x86-64-linux-gnu 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 libidn2-0 libip4tc2 libisl23 libitm1 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblsan0 liblzma5 libmount1 libncurses6 libncursesw6 libnettle8 libpam-modules libpam-modules-bin libpam-runtime libpam0g libperl5.34 libpng16-16 libprocps8 libquadmath0 libreadline8 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 util-linux xz-utils zlib1g 130 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. Need to get 156 MB of archives. After this operation, 201 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcrypt-dev amd64 1:4.4.28-2 [112 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libc6-dev amd64 2.36-0ubuntu2 [2085 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libc-dev-bin amd64 2.36-0ubuntu2 [19.9 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcrypt1 amd64 1:4.4.28-2 [80.0 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 linux-libc-dev amd64 5.19.0-15.15 [1294 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libtirpc-common all 1.3.3+ds-1 [7790 B] Get:7 http://ftpmaster.internal/ubuntu kinetic/main amd64 libk5crypto3 amd64 1.20-1 [81.2 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgssapi-krb5-2 amd64 1.20-1 [142 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic/main amd64 libkrb5-3 amd64 1.20-1 [346 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic/main amd64 libkrb5support0 amd64 1.20-1 [31.2 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcom-err2 amd64 1.46.5-2ubuntu2 [9074 B] Get:12 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libkeyutils1 amd64 1.6.3-1 [10.7 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libssl3 amd64 3.0.5-2ubuntu1 [1893 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libtirpc-dev amd64 1.3.3+ds-1 [193 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libtirpc3 amd64 1.3.3+ds-1 [80.9 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libc6 amd64 2.36-0ubuntu2 [3163 kB] Get:17 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libc-bin amd64 2.36-0ubuntu2 [676 kB] Get:18 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libatomic1 amd64 12.2.0-1ubuntu1 [10.4 kB] Get:19 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libubsan1 amd64 12.2.0-1ubuntu1 [969 kB] Get:20 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libquadmath0 amd64 12.2.0-1ubuntu1 [152 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 liblsan0 amd64 12.2.0-1ubuntu1 [1060 kB] Get:22 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libitm1 amd64 12.2.0-1ubuntu1 [29.4 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libgomp1 amd64 12.2.0-1ubuntu1 [125 kB] Get:24 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 gcc-12-base amd64 12.2.0-1ubuntu1 [19.2 kB] Get:25 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libgcc-s1 amd64 12.2.0-1ubuntu1 [54.2 kB] Get:26 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libcc1-0 amd64 12.2.0-1ubuntu1 [46.4 kB] Get:27 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libstdc++6 amd64 12.2.0-1ubuntu1 [678 kB] Get:28 http://ftpmaster.internal/ubuntu kinetic/main amd64 base-files amd64 12.2ubuntu2 [73.2 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic/main amd64 bsdutils amd64 1:2.38-4ubuntu1 [80.7 kB] Get:30 http://ftpmaster.internal/ubuntu kinetic/main amd64 debianutils amd64 5.7-0.3 [103 kB] Get:31 http://ftpmaster.internal/ubuntu kinetic/main amd64 libzstd1 amd64 1.5.2+dfsg-1 [270 kB] Get:32 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgpg-error0 amd64 1.45-2 [69.0 kB] Get:33 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgcrypt20 amd64 1.10.1-2ubuntu1 [524 kB] Get:34 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblzma5 amd64 5.2.5-2.1 [99.2 kB] Get:35 http://ftpmaster.internal/ubuntu kinetic/main amd64 libblkid1 amd64 2.38-4ubuntu1 [103 kB] Get:36 http://ftpmaster.internal/ubuntu kinetic/main amd64 libuuid1 amd64 2.38-4ubuntu1 [23.2 kB] Get:37 http://ftpmaster.internal/ubuntu kinetic/main amd64 libfdisk1 amd64 2.38-4ubuntu1 [144 kB] Get:38 http://ftpmaster.internal/ubuntu kinetic/main amd64 systemd-sysv amd64 251.2-2ubuntu2 [11.2 kB] Get:39 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libapparmor1 amd64 3.0.7-1ubuntu1 [36.5 kB] Get:40 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcryptsetup12 amd64 2:2.5.0-1ubuntu1 [220 kB] Get:41 http://ftpmaster.internal/ubuntu kinetic/main amd64 libip4tc2 amd64 1.8.7-1ubuntu6 [19.7 kB] Get:42 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libkmod2 amd64 30+20220630-3ubuntu1 [48.9 kB] Get:43 http://ftpmaster.internal/ubuntu kinetic/main amd64 libselinux1 amd64 3.4-1 [77.6 kB] Get:44 http://ftpmaster.internal/ubuntu kinetic/main amd64 libmount1 amd64 2.38-4ubuntu1 [121 kB] Get:45 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libpam0g amd64 1.5.2-2ubuntu1 [60.2 kB] Get:46 http://ftpmaster.internal/ubuntu kinetic/main amd64 mount amd64 2.38-4ubuntu1 [114 kB] Get:47 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsemanage-common all 3.4-1 [9828 B] Get:48 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsepol2 amd64 3.4-2 [294 kB] Get:49 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsemanage2 amd64 3.4-1 [91.8 kB] Get:50 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libpam-modules-bin amd64 1.5.2-2ubuntu1 [44.8 kB] Get:51 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libpam-modules amd64 1.5.2-2ubuntu1 [283 kB] Get:52 http://ftpmaster.internal/ubuntu kinetic/main amd64 passwd amd64 1:4.11.1+dfsg1-2ubuntu1 [765 kB] Get:53 http://ftpmaster.internal/ubuntu kinetic/main amd64 adduser all 3.121ubuntu1 [150 kB] Get:54 http://ftpmaster.internal/ubuntu kinetic/main amd64 systemd amd64 251.2-2ubuntu2 [4742 kB] Get:55 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsystemd0 amd64 251.2-2ubuntu2 [326 kB] Get:56 http://ftpmaster.internal/ubuntu kinetic/main amd64 libudev1 amd64 251.2-2ubuntu2 [81.3 kB] Get:57 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 zlib1g amd64 1:1.2.11.dfsg-4.1ubuntu1 [58.8 kB] Get:58 http://ftpmaster.internal/ubuntu kinetic/main amd64 libapt-pkg6.0 amd64 2.5.2 [903 kB] Get:59 http://ftpmaster.internal/ubuntu kinetic/main amd64 dpkg amd64 1.21.9ubuntu1 [1334 kB] Get:60 http://ftpmaster.internal/ubuntu kinetic/main amd64 dash amd64 0.5.11+git20210903+057cd650a4ed-8ubuntu1 [88.2 kB] Get:61 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 diffutils amd64 1:3.8-1 [174 kB] Get:62 http://ftpmaster.internal/ubuntu kinetic/main amd64 findutils amd64 4.9.0-3ubuntu1 [294 kB] Get:63 http://ftpmaster.internal/ubuntu kinetic/main amd64 gzip amd64 1.12-1ubuntu1 [98.4 kB] Get:64 http://ftpmaster.internal/ubuntu kinetic/main amd64 login amd64 1:4.11.1+dfsg1-2ubuntu1 [183 kB] Get:65 http://ftpmaster.internal/ubuntu kinetic/main amd64 ncurses-bin amd64 6.3+20220423-2 [183 kB] Get:66 http://ftpmaster.internal/ubuntu kinetic/main amd64 libperl5.34 amd64 5.34.0-5ubuntu1 [4691 kB] Get:67 http://ftpmaster.internal/ubuntu kinetic/main amd64 perl amd64 5.34.0-5ubuntu1 [231 kB] Get:68 http://ftpmaster.internal/ubuntu kinetic/main amd64 perl-base amd64 5.34.0-5ubuntu1 [1739 kB] Get:69 http://ftpmaster.internal/ubuntu kinetic/main amd64 perl-modules-5.34 all 5.34.0-5ubuntu1 [2952 kB] Get:70 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.10 [721 kB] Get:71 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsmartcols1 amd64 2.38-4ubuntu1 [50.8 kB] Get:72 http://ftpmaster.internal/ubuntu kinetic/main amd64 util-linux-extra amd64 2.38-4ubuntu1 [83.8 kB] Get:73 http://ftpmaster.internal/ubuntu kinetic/main amd64 util-linux amd64 2.38-4ubuntu1 [1069 kB] Get:74 http://ftpmaster.internal/ubuntu kinetic/main amd64 base-passwd amd64 3.6.0 [49.8 kB] Get:75 http://ftpmaster.internal/ubuntu kinetic/main amd64 init-system-helpers all 1.64 [38.7 kB] Get:76 http://ftpmaster.internal/ubuntu kinetic/main amd64 ncurses-base all 6.3+20220423-2 [21.2 kB] Get:77 http://ftpmaster.internal/ubuntu kinetic/main amd64 libnettle8 amd64 3.8.1-2 [172 kB] Get:78 http://ftpmaster.internal/ubuntu kinetic/main amd64 libhogweed6 amd64 3.8.1-2 [199 kB] Get:79 http://ftpmaster.internal/ubuntu kinetic/main amd64 sgml-base all 1.30 [12.5 kB] Get:80 http://ftpmaster.internal/ubuntu kinetic/main amd64 libidn2-0 amd64 2.3.3-1 [62.9 kB] Get:81 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgnutls30 amd64 3.7.7-2ubuntu1 [981 kB] Get:82 http://ftpmaster.internal/ubuntu kinetic/main amd64 gpgv amd64 2.2.35-3ubuntu1 [137 kB] Get:83 http://ftpmaster.internal/ubuntu kinetic/main amd64 apt amd64 2.5.2 [1377 kB] Get:84 http://ftpmaster.internal/ubuntu kinetic/main amd64 logsave amd64 1.46.5-2ubuntu2 [9914 B] Get:85 http://ftpmaster.internal/ubuntu kinetic/main amd64 libext2fs2 amd64 1.46.5-2ubuntu2 [205 kB] Get:86 http://ftpmaster.internal/ubuntu kinetic/main amd64 e2fsprogs amd64 1.46.5-2ubuntu2 [585 kB] Get:87 http://ftpmaster.internal/ubuntu kinetic/main amd64 init amd64 1.64 [5536 B] Get:88 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcap-ng0 amd64 0.8.3-1 [15.7 kB] Get:89 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libpam-runtime all 1.5.2-2ubuntu1 [40.0 kB] Get:90 http://ftpmaster.internal/ubuntu kinetic/main amd64 libncurses6 amd64 6.3+20220423-2 [110 kB] Get:91 http://ftpmaster.internal/ubuntu kinetic/main amd64 libncursesw6 amd64 6.3+20220423-2 [146 kB] Get:92 http://ftpmaster.internal/ubuntu kinetic/main amd64 libtinfo6 amd64 6.3+20220423-2 [99.6 kB] Get:93 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 lsb-base all 11.2ubuntu1 [12.4 kB] Get:94 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libprocps8 amd64 2:3.3.17-7ubuntu1 [35.3 kB] Get:95 http://ftpmaster.internal/ubuntu kinetic/main amd64 libss2 amd64 1.46.5-2ubuntu2 [12.3 kB] Get:96 http://ftpmaster.internal/ubuntu kinetic/main amd64 mawk amd64 1.3.4.20200120-3.1 [109 kB] Get:97 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 procps amd64 2:3.3.17-7ubuntu1 [374 kB] Get:98 http://ftpmaster.internal/ubuntu kinetic/main amd64 readline-common all 8.1.2-1.2 [53.6 kB] Get:99 http://ftpmaster.internal/ubuntu kinetic/main amd64 libreadline8 amd64 8.1.2-1.2 [153 kB] Get:100 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsqlite3-0 amd64 3.39.2-1 [654 kB] Get:101 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 openssl amd64 3.0.5-2ubuntu1 [1178 kB] Get:102 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpng16-16 amd64 1.6.37-5 [187 kB] Get:103 http://ftpmaster.internal/ubuntu kinetic/main amd64 xz-utils amd64 5.2.5-2.1 [83.8 kB] Get:104 http://ftpmaster.internal/ubuntu kinetic/main amd64 advancecomp amd64 2.3-1 [175 kB] Get:105 http://ftpmaster.internal/ubuntu kinetic/main amd64 libctf0 amd64 2.39-1ubuntu1 [97.3 kB] Get:106 http://ftpmaster.internal/ubuntu kinetic/main amd64 libctf-nobfd0 amd64 2.39-1ubuntu1 [99.7 kB] Get:107 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgprofng0 amd64 2.39-1ubuntu1 [898 kB] Get:108 http://ftpmaster.internal/ubuntu kinetic/main amd64 libbinutils amd64 2.39-1ubuntu1 [608 kB] Get:109 http://ftpmaster.internal/ubuntu kinetic/main amd64 binutils amd64 2.39-1ubuntu1 [3292 B] Get:110 http://ftpmaster.internal/ubuntu kinetic/main amd64 binutils-common amd64 2.39-1ubuntu1 [224 kB] Get:111 http://ftpmaster.internal/ubuntu kinetic/main amd64 binutils-x86-64-linux-gnu amd64 2.39-1ubuntu1 [2435 kB] Get:112 http://ftpmaster.internal/ubuntu kinetic/main amd64 libisl23 amd64 0.25-1 [740 kB] Get:113 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 cpp-12 amd64 12.2.0-1ubuntu1 [10.6 MB] Get:114 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libasan8 amd64 12.2.0-1ubuntu1 [2432 kB] Get:115 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libtsan2 amd64 12.2.0-1ubuntu1 [2456 kB] Get:116 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libgcc-12-dev amd64 12.2.0-1ubuntu1 [2577 kB] Get:117 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 gcc-12 amd64 12.2.0-1ubuntu1 [21.4 MB] Get:118 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libstdc++-12-dev amd64 12.2.0-1ubuntu1 [2158 kB] Get:119 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 g++-12 amd64 12.2.0-1ubuntu1 [12.0 MB] Get:120 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 g++ amd64 4:12.1.0-3ubuntu1 [1414 B] Get:121 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 gcc amd64 4:12.1.0-3ubuntu1 [5112 B] Get:122 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 cpp amd64 4:12.1.0-3ubuntu1 [27.4 kB] Get:123 http://ftpmaster.internal/ubuntu kinetic/main amd64 g++-11 amd64 11.3.0-5ubuntu1 [11.3 MB] Get:124 http://ftpmaster.internal/ubuntu kinetic/main amd64 libstdc++-11-dev amd64 11.3.0-5ubuntu1 [2079 kB] Get:125 http://ftpmaster.internal/ubuntu kinetic/main amd64 libasan6 amd64 11.3.0-5ubuntu1 [2264 kB] Get:126 http://ftpmaster.internal/ubuntu kinetic/main amd64 gcc-11 amd64 11.3.0-5ubuntu1 [20.0 MB] Get:127 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgcc-11-dev amd64 11.3.0-5ubuntu1 [2486 kB] Get:128 http://ftpmaster.internal/ubuntu kinetic/main amd64 libtsan0 amd64 11.3.0-5ubuntu1 [2240 kB] Get:129 http://ftpmaster.internal/ubuntu kinetic/main amd64 cpp-11 amd64 11.3.0-5ubuntu1 [9911 kB] Get:130 http://ftpmaster.internal/ubuntu kinetic/main amd64 gcc-11-base amd64 11.3.0-5ubuntu1 [20.4 kB] Get:131 http://ftpmaster.internal/ubuntu kinetic/main amd64 dpkg-dev all 1.21.9ubuntu1 [1070 kB] Get:132 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdpkg-perl all 1.21.9ubuntu1 [237 kB] Get:133 http://ftpmaster.internal/ubuntu kinetic/main amd64 lto-disabled-list all 32 [12.2 kB] Get:134 http://ftpmaster.internal/ubuntu kinetic/main amd64 libfakeroot amd64 1.29-1ubuntu1 [31.1 kB] Get:135 http://ftpmaster.internal/ubuntu kinetic/main amd64 fakeroot amd64 1.29-1ubuntu1 [60.0 kB] Get:136 http://ftpmaster.internal/ubuntu kinetic/main amd64 libassuan0 amd64 2.5.5-4 [37.2 kB] Get:137 http://ftpmaster.internal/ubuntu kinetic/main amd64 pinentry-curses amd64 1.2.0-2ubuntu1 [34.5 kB] Get:138 http://ftpmaster.internal/ubuntu kinetic/main amd64 gpg amd64 2.2.35-3ubuntu1 [522 kB] Get:139 http://ftpmaster.internal/ubuntu kinetic/main amd64 gpgconf amd64 2.2.35-3ubuntu1 [93.6 kB] Get:140 http://ftpmaster.internal/ubuntu kinetic/main amd64 gpg-agent amd64 2.2.35-3ubuntu1 [215 kB] Get:141 http://ftpmaster.internal/ubuntu kinetic/main amd64 policyrcd-script-zg2 all 0.1-3.1 [5730 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 156 MB in 1s (150 MB/s) (Reading database ... 13449 files and directories currently installed.) 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-24304738 amd64 kinetic-proposed -c chroot:build-PACKAGEBUILD-24304738 --arch=amd64 --dist=kinetic-proposed --nolog -A khmer_2.1.2+dfsg-11.dsc Initiating build PACKAGEBUILD-24304738 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-124-generic #140-Ubuntu SMP Thu Aug 4 02:23:37 UTC 2022 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-087.buildd +==============================================================================+ | khmer 2.1.2+dfsg-11 (amd64) Mon, 22 Aug 2022 17:18:56 +0000 | +==============================================================================+ Package: khmer Version: 2.1.2+dfsg-11 Source Version: 2.1.2+dfsg-11 Distribution: kinetic-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-24304738/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/khmer-rlkaTu/resolver-jBUrPH' 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-rlkaTu/khmer-2.1.2+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/khmer-rlkaTu' 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 (159 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: 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. Need to get 51.7 MB of archives. After this operation, 212 MB of additional disk space will be used. 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1.5.0-1.1 [36.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 51.7 MB in 0s (112 MB/s) Selecting previously unselected package libpython3.10-minimal:amd64. 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Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 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 02:23:37 UTC 2022 amd64 (x86_64) Toolchain package versions: binutils_2.39-1ubuntu1 dpkg-dev_1.21.9ubuntu1 g++-11_11.3.0-5ubuntu1 g++-12_12.2.0-1ubuntu1 gcc-11_11.3.0-5ubuntu1 gcc-12_12.2.0-1ubuntu1 libc6-dev_2.36-0ubuntu2 libstdc++-11-dev_11.3.0-5ubuntu1 libstdc++-12-dev_12.2.0-1ubuntu1 libstdc++6_12.2.0-1ubuntu1 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-common_2.39-1ubuntu1 binutils-x86-64-linux-gnu_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_12.2.0-1ubuntu1 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_12.2.0-1ubuntu1 gcc_4:12.1.0-3ubuntu1 gcc-11_11.3.0-5ubuntu1 gcc-11-base_11.3.0-5ubuntu1 gcc-12_12.2.0-1ubuntu1 gcc-12-base_12.2.0-1ubuntu1 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_12.2.0-1ubuntu1 libassuan0_2.5.5-4 libatomic1_12.2.0-1ubuntu1 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 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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 libquadmath0_12.2.0-1ubuntu1 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_2.14-1ubuntu1 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_12.2.0-1ubuntu1 libstdc++6_12.2.0-1ubuntu1 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_12.2.0-1ubuntu1 libubsan1_12.2.0-1ubuntu1 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_25ubuntu2 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-24304738 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-24304738 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-24304738 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 amd64 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-x86_64' 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 dh binary --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -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/kfile.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/__init__.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/thread_utils.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/trimming.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/_version.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/khmer_args.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/utils.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/khmer_logger.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer creating /<>/.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_handling.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_cython_parsing.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_countgraph.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/__init__.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_lump.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_counttable.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_scripts.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_cython_assembly.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_labelhash.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_graph.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_filter_abund.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_hll.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_oxli_functions.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_normalize_by_median.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_read_aligner.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_tabletype.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/graph_features.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_functions.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_subset_graph.py -> /<>/.pybuild/cpython3_3.10_khmer/build/khmer/tests creating /<>/.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/build_graph.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/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) 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/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) building 'khmer._khmer' extension creating build creating build/temp.linux-x86_64-3.10 creating build/temp.linux-x86_64-3.10/src creating build/temp.linux-x86_64-3.10/src/khmer creating build/temp.linux-x86_64-3.10/src/oxli creating build/temp.linux-x86_64-3.10/third-party creating build/temp.linux-x86_64-3.10/third-party/smhasher x86_64-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-x86_64-3.10/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/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) : | ^~~~~~~~~~~~~~~~~~~~~~ x86_64-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-x86_64-3.10/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/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) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-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-x86_64-3.10/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) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-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-x86_64-3.10/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/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()); | ^~~~~~~~~~~~~~~~ x86_64-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-x86_64-3.10/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/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(); | ^~~~~ x86_64-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-x86_64-3.10/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, | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-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-x86_64-3.10/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_khmer.cpython-310-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.utils' extension creating build/temp.linux-x86_64-3.10/khmer creating build/temp.linux-x86_64-3.10/khmer/_oxli x86_64-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-x86_64-3.10/khmer/_oxli/utils.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/khmer/_oxli/utils.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/utils.cpython-310-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.graphs' extension x86_64-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-x86_64-3.10/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 | x86_64-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-x86_64-3.10/khmer/_oxli/graphs.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/graphs.cpython-310-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.assembly' extension x86_64-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-x86_64-3.10/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 | x86_64-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-x86_64-3.10/khmer/_oxli/assembly.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.cpython-310-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.parsing' extension x86_64-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-x86_64-3.10/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) { | ~~~~~~~~~~^~~~~~~~~~~ x86_64-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-x86_64-3.10/khmer/_oxli/parsing.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/parsing.cpython-310-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hashing' extension x86_64-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-x86_64-3.10/khmer/_oxli/hashing.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/khmer/_oxli/hashing.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.cpython-310-x86_64-linux-gnu.so -fopenmp running build_scripts creating build/scripts-3.10 copying and adjusting scripts/sample-reads-randomly.py -> build/scripts-3.10 copying and adjusting scripts/filter-abund-single.py -> build/scripts-3.10 copying and adjusting scripts/annotate-partitions.py -> build/scripts-3.10 copying and adjusting scripts/load-graph.py -> build/scripts-3.10 copying and adjusting scripts/extract-long-sequences.py -> build/scripts-3.10 copying and adjusting scripts/make-initial-stoptags.py -> build/scripts-3.10 copying and adjusting scripts/merge-partitions.py -> build/scripts-3.10 copying and adjusting scripts/filter-stoptags.py -> build/scripts-3.10 copying and adjusting scripts/readstats.py -> build/scripts-3.10 copying and adjusting scripts/extract-paired-reads.py -> build/scripts-3.10 copying and adjusting scripts/abundance-dist-single.py -> build/scripts-3.10 copying and adjusting scripts/trim-low-abund.py -> build/scripts-3.10 copying and adjusting scripts/split-paired-reads.py -> build/scripts-3.10 copying and adjusting scripts/interleave-reads.py -> build/scripts-3.10 copying and adjusting scripts/abundance-dist.py -> build/scripts-3.10 copying and adjusting scripts/normalize-by-median.py -> build/scripts-3.10 copying and adjusting scripts/filter-abund.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/do-partition.py -> build/scripts-3.10 copying and adjusting scripts/unique-kmers.py -> build/scripts-3.10 copying and adjusting scripts/extract-partitions.py -> build/scripts-3.10 copying and adjusting scripts/partition-graph.py -> build/scripts-3.10 copying and adjusting scripts/fastq-to-fasta.py -> build/scripts-3.10 copying and adjusting scripts/count-median.py -> build/scripts-3.10 changing mode of build/scripts-3.10/sample-reads-randomly.py from 644 to 755 changing mode of build/scripts-3.10/filter-abund-single.py from 644 to 755 changing mode of build/scripts-3.10/annotate-partitions.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/extract-long-sequences.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/merge-partitions.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/readstats.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/abundance-dist-single.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/split-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/abundance-dist.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/filter-abund.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/do-partition.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/extract-partitions.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/fastq-to-fasta.py from 644 to 755 changing mode of build/scripts-3.10/count-median.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/utils.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/graphs.cpp' Cython extension (up-to-date) 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) building 'khmer._khmer' extension x86_64-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-x86_64-3.10/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/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) : | ^~~~~~~~~~~~~~~~~~~~~~ x86_64-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-x86_64-3.10/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/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) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-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-x86_64-3.10/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) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-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-x86_64-3.10/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/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()); | ^~~~~~~~~~~~~~~~ x86_64-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-x86_64-3.10/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/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(); | ^~~~~ x86_64-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-x86_64-3.10/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, | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-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-x86_64-3.10/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp creating build/lib.linux-x86_64-3.10 creating build/lib.linux-x86_64-3.10/khmer x86_64-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-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.10/khmer/_khmer.cpython-310-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.utils' extension x86_64-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-x86_64-3.10/khmer/_oxli/utils.o -O3 -std=c++11 -pedantic -fopenmp creating build/lib.linux-x86_64-3.10/khmer/_oxli x86_64-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-x86_64-3.10/khmer/_oxli/utils.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.10/khmer/_oxli/utils.cpython-310-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.graphs' extension x86_64-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-x86_64-3.10/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 | x86_64-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-x86_64-3.10/khmer/_oxli/graphs.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.10/khmer/_oxli/graphs.cpython-310-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.assembly' extension x86_64-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-x86_64-3.10/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 | x86_64-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-x86_64-3.10/khmer/_oxli/assembly.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.10/khmer/_oxli/assembly.cpython-310-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.parsing' extension x86_64-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-x86_64-3.10/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) { | ~~~~~~~~~~^~~~~~~~~~~ x86_64-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-x86_64-3.10/khmer/_oxli/parsing.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.10/khmer/_oxli/parsing.cpython-310-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hashing' extension x86_64-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-x86_64-3.10/khmer/_oxli/hashing.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/khmer/_oxli/hashing.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.10/khmer/_oxli/hashing.cpython-310-x86_64-linux-gnu.so -fopenmp copying build/lib.linux-x86_64-3.10/khmer/_khmer.cpython-310-x86_64-linux-gnu.so -> khmer copying build/lib.linux-x86_64-3.10/khmer/_oxli/utils.cpython-310-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-3.10/khmer/_oxli/graphs.cpython-310-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-3.10/khmer/_oxli/assembly.cpython-310-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-3.10/khmer/_oxli/parsing.cpython-310-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-3.10/khmer/_oxli/hashing.cpython-310-x86_64-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 sample-reads-randomly.py script to /<>/fakehome/.local/bin Installing filter-abund-single.py script to /<>/fakehome/.local/bin Installing annotate-partitions.py script to /<>/fakehome/.local/bin Installing load-graph.py script to /<>/fakehome/.local/bin Installing extract-long-sequences.py script to /<>/fakehome/.local/bin Installing make-initial-stoptags.py script to /<>/fakehome/.local/bin Installing merge-partitions.py script to /<>/fakehome/.local/bin Installing filter-stoptags.py script to /<>/fakehome/.local/bin Installing readstats.py script to /<>/fakehome/.local/bin Installing extract-paired-reads.py script to /<>/fakehome/.local/bin Installing abundance-dist-single.py script to /<>/fakehome/.local/bin Installing trim-low-abund.py script to /<>/fakehome/.local/bin Installing split-paired-reads.py script to /<>/fakehome/.local/bin Installing interleave-reads.py script to /<>/fakehome/.local/bin Installing abundance-dist.py script to /<>/fakehome/.local/bin Installing normalize-by-median.py script to /<>/fakehome/.local/bin Installing filter-abund.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 do-partition.py script to /<>/fakehome/.local/bin Installing unique-kmers.py script to /<>/fakehome/.local/bin Installing extract-partitions.py script to /<>/fakehome/.local/bin Installing partition-graph.py script to /<>/fakehome/.local/bin Installing fastq-to-fasta.py script to /<>/fakehome/.local/bin Installing count-median.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-common.debhelper.log 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/utils.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/graphs.cpp' Cython extension (up-to-date) 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) building 'khmer._khmer' extension x86_64-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-x86_64-3.10/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/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) : | ^~~~~~~~~~~~~~~~~~~~~~ x86_64-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-x86_64-3.10/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/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) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-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-x86_64-3.10/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) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-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-x86_64-3.10/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/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()); | ^~~~~~~~~~~~~~~~ x86_64-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-x86_64-3.10/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/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(); | ^~~~~ x86_64-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-x86_64-3.10/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, | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-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-x86_64-3.10/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_khmer.cpython-310-x86_64-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/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/assembly.pxd -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.cpython-310-x86_64-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/__init__.py -> /<>/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/graphs.cpp -> /<>/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/graphs.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/graphs.pyx -> /<>/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/utils.cpython-310-x86_64-linux-gnu.so -> /<>/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/parsing.cpython-310-x86_64-linux-gnu.so -> /<>/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/parsing.cpp -> /<>/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/graphs.cpython-310-x86_64-linux-gnu.so -> /<>/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/hashing.cpp -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.cpython-310-x86_64-linux-gnu.so -> /<>/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/hashing.pyx -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli 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/thread_utils.py -> /<>/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_version.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_streaming_io.py -> /<>/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_countgraph.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/test_lump.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_counttable.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/.gitignore -> /<>/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_script_output.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_nibblestorage.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_threaded_sequence_processor.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/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_filter_abund.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_hll.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 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-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/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/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/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/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/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-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/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/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/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/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/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/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/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/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/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/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/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/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/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/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 -> /<>/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/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/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/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/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.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/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/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/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/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/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/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/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/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/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/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/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/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/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/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-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/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-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/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/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/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/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/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/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/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-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 -> /<>/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/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/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/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/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/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/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/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-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/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/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/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-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-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/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/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-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/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/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/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/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/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/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/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-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-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/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/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/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-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/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/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/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/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/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/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-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-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/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/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/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/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/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/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/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/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-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/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/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/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/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/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/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/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-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/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/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-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/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/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/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-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-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/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/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_oxli_functions.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_normalize_by_median.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_read_aligner.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_tabletype.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests 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/khmer_tst_utils.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_subset_graph.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests 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/_version.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/utils.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer 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-x86_64-linux-gnu.so -> /<>/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/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/build_graph.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/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/__init__.py to __init__.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/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_handling.py to test_read_handling.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_cython_parsing.py to test_cython_parsing.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/__init__.py to __init__.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/test_sequence_validation.py to test_sequence_validation.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_cpython_hierarchy.py to test_cpython_hierarchy.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_script_output.py to test_script_output.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_nibblestorage.py to test_nibblestorage.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_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_graph.py to test_graph.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_filter_abund.py to test_filter_abund.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_hll.py to test_hll.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_oxli_functions.py to test_oxli_functions.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_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_script_arguments.py to test_script_arguments.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_hashset.py to test_hashset.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/graph_features.py to graph_features.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_functions.py to test_functions.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/trimming.py to trimming.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/khmer_args.py to khmer_args.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/khmer_logger.py to khmer_logger.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/build_graph.py to build_graph.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/sample-reads-randomly.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/filter-abund-single.py -> /<>/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/load-graph.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/make-initial-stoptags.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-stoptags.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/extract-paired-reads.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/trim-low-abund.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/interleave-reads.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/normalize-by-median.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/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/do-partition.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/extract-partitions.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/fastq-to-fasta.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/count-median.py -> /<>/debian/khmer/usr/lib/khmer/bin changing mode of /<>/debian/khmer/usr/lib/khmer/bin/sample-reads-randomly.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/filter-abund-single.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/annotate-partitions.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/extract-long-sequences.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/merge-partitions.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/readstats.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/abundance-dist-single.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/split-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/abundance-dist.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/filter-abund.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/do-partition.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/extract-partitions.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/fastq-to-fasta.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/count-median.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 60.55s (0:01:00) ===== rm -fr -- /tmp/dh-xdg-rundir-Ly2uUyAM make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild rm -f -- debian/khmer-common.substvars debian/khmer.substvars debian/liboxli1.substvars debian/liboxli-dev.substvars rm -fr -- debian/.debhelper/generated/khmer-common/ debian/khmer-common/ debian/tmp/ debian/.debhelper/generated/khmer/ debian/khmer/ debian/.debhelper/generated/liboxli1/ debian/liboxli1/ debian/.debhelper/generated/liboxli-dev/ debian/liboxli-dev/ dh_auto_install -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/utils.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/graphs.cpp' Cython extension (up-to-date) 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) building 'khmer._khmer' extension x86_64-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-x86_64-3.10/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/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) : | ^~~~~~~~~~~~~~~~~~~~~~ x86_64-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-x86_64-3.10/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/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) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-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-x86_64-3.10/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) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-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-x86_64-3.10/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/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()); | ^~~~~~~~~~~~~~~~ x86_64-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-x86_64-3.10/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/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(); | ^~~~~ x86_64-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-x86_64-3.10/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, | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-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-x86_64-3.10/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp x86_64-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-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_khmer.cpython-310-x86_64-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/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/assembly.pxd -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.cpython-310-x86_64-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/__init__.py -> /<>/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/graphs.cpp -> /<>/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/graphs.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/graphs.pyx -> /<>/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 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/utils.cpython-310-x86_64-linux-gnu.so -> /<>/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/parsing.cpython-310-x86_64-linux-gnu.so -> /<>/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/parsing.cpp -> /<>/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/graphs.cpython-310-x86_64-linux-gnu.so -> /<>/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/hashing.cpp -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.cpython-310-x86_64-linux-gnu.so -> /<>/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/hashing.pyx -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli 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/thread_utils.py -> /<>/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_version.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_streaming_io.py -> /<>/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_countgraph.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/test_lump.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_counttable.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/.gitignore -> /<>/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_script_output.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_nibblestorage.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_threaded_sequence_processor.py -> /<>/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_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_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_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_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_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__/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_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/__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_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_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_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_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__/__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_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_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_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_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_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_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_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__/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__/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_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_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__/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_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_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__/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_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_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_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/test_graph.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_filter_abund.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_hll.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 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-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/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/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/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/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/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-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/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/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/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/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/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/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/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/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/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/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/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/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/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/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 -> /<>/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/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/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/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/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.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/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/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/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/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/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/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/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/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/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/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/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/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/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/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-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/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-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/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/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/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/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/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/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/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-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 -> /<>/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/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/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/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/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/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/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/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-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/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/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/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-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-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/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/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-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/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/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/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/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/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/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/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-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-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/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/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/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-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/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/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/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/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/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/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-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-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/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/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/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/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/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/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/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/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-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/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/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/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/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/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/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/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-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/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/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-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/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/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/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-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-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/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/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_oxli_functions.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_normalize_by_median.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_read_aligner.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_tabletype.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests 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/khmer_tst_utils.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_subset_graph.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests creating /<>/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__ 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__/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__/utils.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__/_version.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/trimming.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer 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/khmer_args.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/khmer_logger.py -> /<>/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /<>/.pybuild/cpython3_3.10_khmer/build/khmer/_khmer.cpython-310-x86_64-linux-gnu.so -> /<>/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/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 creating /<>/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__/__init__.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/build_graph.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/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/__init__.py to __init__.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/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_handling.py to test_read_handling.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_cython_parsing.py to test_cython_parsing.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/__init__.py to __init__.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/test_sequence_validation.py to test_sequence_validation.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_cpython_hierarchy.py to test_cpython_hierarchy.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_script_output.py to test_script_output.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_nibblestorage.py to test_nibblestorage.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_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_graph.py to test_graph.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_filter_abund.py to test_filter_abund.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_hll.py to test_hll.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_oxli_functions.py to test_oxli_functions.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_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_script_arguments.py to test_script_arguments.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_hashset.py to test_hashset.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/graph_features.py to graph_features.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_functions.py to test_functions.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/trimming.py to trimming.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/khmer_args.py to khmer_args.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/khmer_logger.py to khmer_logger.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/build_graph.py to build_graph.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/sample-reads-randomly.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/filter-abund-single.py -> /<>/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/load-graph.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/make-initial-stoptags.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-stoptags.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/extract-paired-reads.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/trim-low-abund.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/interleave-reads.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/normalize-by-median.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/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/do-partition.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/extract-partitions.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/fastq-to-fasta.py -> /<>/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/count-median.py -> /<>/debian/khmer/usr/lib/khmer/bin changing mode of /<>/debian/khmer/usr/lib/khmer/bin/sample-reads-randomly.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/filter-abund-single.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/annotate-partitions.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/extract-long-sequences.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/merge-partitions.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/readstats.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/abundance-dist-single.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/split-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/abundance-dist.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/filter-abund.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/do-partition.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/extract-partitions.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/fastq-to-fasta.py to 755 changing mode of /<>/debian/khmer/usr/lib/khmer/bin/count-median.py to 755 rm -f debian/khmer-common.debhelper.log 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/khmer-common/usr/share/file/khmer cp --reflink=auto -a ./include/oxli/magic debian/khmer-common/usr/share/file/khmer/ 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/x86_64-linux-gnu cp --reflink=auto -a ./src/oxli/liboxli.so.1 debian/liboxli1/usr/lib/x86_64-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/x86_64-linux-gnu cp --reflink=auto -a ./src/oxli/liboxli.a ./src/oxli/liboxli.so debian/liboxli-dev/usr/lib/x86_64-linux-gnu/ install -d debian/liboxli-dev/usr/lib/x86_64-linux-gnu/pkgconfig cp --reflink=auto -a ./src/oxli/oxli.pc debian/liboxli-dev/usr/lib/x86_64-linux-gnu/pkgconfig/ install -d debian/.debhelper/generated/liboxli-dev find debian/khmer -name .gitignore -delete make[1]: Leaving directory '/<>' dh_installdocs -O--buildsystem=pybuild install -d debian/khmer-common/usr/share/doc/khmer-common cd './build/sphinx/html/..' && find 'html' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /<>/debian/khmer-common/usr/share/doc/khmer-common cp --reflink=auto -a ./CITATION debian/khmer-common/usr/share/doc/khmer-common cp --reflink=auto -a ./README.rst debian/khmer-common/usr/share/doc/khmer-common cp --reflink=auto -a ./debian/README.test debian/khmer-common/usr/share/doc/khmer-common cp --reflink=auto -a ./debian/tests/run-unit-test debian/khmer-common/usr/share/doc/khmer-common cp --reflink=auto -a ./src/oxli/test-compile.cc debian/khmer-common/usr/share/doc/khmer-common chmod -R u\+rw,go=rX debian/khmer-common/usr/share/doc install -p -m0644 debian/copyright debian/khmer-common/usr/share/doc/khmer-common/copyright install -d debian/khmer-common/usr/share/doc-base/ install -p -m0644 debian/doc-base debian/khmer-common/usr/share/doc-base/khmer-common.khmer 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-common.debhelper.log debian/khmer.debhelper.log debian/liboxli-dev.debhelper.log debian/liboxli1.debhelper.log debian/rules override_dh_sphinxdoc make[1]: Entering directory '/<>' dh_sphinxdoc dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/khmer-common/usr/share/doc/khmer-common/html/_static/labibi.js ln -sf ../../../../javascript/sphinxdoc/1.0/doctools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.js ln -sf ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js ln -sf ../../../../javascript/sphinxdoc/1.0/language_data.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js ln -sf ../../../../javascript/sphinxdoc/1.0/underscore.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js ln -sf ../../../../javascript/sphinxdoc/1.0/jquery.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/.buildinfo mv debian/khmer-common.substvars.new debian/khmer-common.substvars mv debian/khmer-common.substvars.new debian/khmer-common.substvars mv debian/khmer-common.substvars.new debian/khmer-common.substvars mv debian/khmer-common.substvars.new debian/khmer-common.substvars mv debian/khmer-common.substvars.new debian/khmer-common.substvars rdfind -makesymlinks true -followsymlinks true\ /usr/lib/python3/dist-packages/guzzle_sphinx_theme \ debian/khmer-common debian/khmer-common/usr debian/khmer-common/usr/share debian/khmer-common/usr/share/doc-base debian/khmer-common/usr/share/doc-base/khmer-common.khmer debian/khmer-common/usr/share/doc debian/khmer-common/usr/share/doc/khmer-common debian/khmer-common/usr/share/doc/khmer-common/test-compile.cc debian/khmer-common/usr/share/doc/khmer-common/README.test debian/khmer-common/usr/share/doc/khmer-common/html debian/khmer-common/usr/share/doc/khmer-common/html/roadmap.html debian/khmer-common/usr/share/doc/khmer-common/html/_static debian/khmer-common/usr/share/doc/khmer-common/html/_static/pygments.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/js debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.min.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/documentation_options.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/basic.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/css debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/bootstrap-theme.min.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/font-face.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/bootstrap.min.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/labibi.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.woff 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debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/index.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.0.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.2.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-2.0.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-2.1.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.3.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/LICENSE.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/introduction.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/roadmap.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/contributors.html debian/khmer-common/usr/share/doc/khmer-common/html/.buildinfo debian/khmer-common/usr/share/doc/khmer-common/README.rst debian/khmer-common/usr/share/doc/khmer-common/run-unit-test debian/khmer-common/usr/share/doc/khmer-common/copyright debian/khmer-common/usr/share/file debian/khmer-common/usr/share/file/khmer debian/khmer-common/usr/share/file/khmer/magic Now scanning "/usr/lib/python3/dist-packages/guzzle_sphinx_theme", found 116 files. Now scanning "debian/khmer-common"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js , found 195 files. Now scanning "debian/khmer-common/usr"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js , found 195 files. Now scanning "debian/khmer-common/usr/share"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js , found 195 files. Now scanning "debian/khmer-common/usr/share/doc-base", found 1 files. Now scanning "debian/khmer-common/usr/share/doc-base/khmer-common.khmer", found 1 files. Now scanning "debian/khmer-common/usr/share/doc"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js , found 193 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js , found 193 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/test-compile.cc", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/README.test", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js , found 187 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/roadmap.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js , found 99 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/pygments.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/js", found 2 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.min.js", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.js", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js , found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/documentation_options.js", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/basic.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js , found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/css", found 3 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/bootstrap-theme.min.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/font-face.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/bootstrap.min.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js , found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/labibi.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts", found 84 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSans-Italic.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSerif-Regular.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSans-Regular.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro", found 35 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/ReadMe.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/bower.json", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/SourceSerifProReadMe.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF", found 6 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Light.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Bold.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-ExtraLight.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Semibold.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Regular.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Black.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF", found 12 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF", found 6 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Light.ttf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Bold.ttf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Semibold.ttf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Black.ttf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-ExtraLight.ttf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Regular.ttf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF", found 6 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Bold.otf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-ExtraLight.otf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Regular.otf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Black.otf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Semibold.otf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Light.otf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF", found 6 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Light.otf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Semibold.otf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-ExtraLight.otf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Black.otf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Regular.otf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Bold.otf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/source-serif-pro.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT", found 6 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Regular.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Black.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Light.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-ExtraLight.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Bold.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Semibold.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/README.md", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.woff2", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans", found 41 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/stylesheet.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts", found 40 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/file.png", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/labibi.js", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js , found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/plus.png", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/minus.png", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js , found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/guzzle.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_images", found 2 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_images/partitioning-workflow.png", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_images/artifact-removal.png", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user", found 13 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/api-examples.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/getting-help.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/scripts.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/biblio.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/examples.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/guide.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/choosing-table-sizes.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/galaxy.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/install.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/known-issues.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/index.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/blog-posts.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/partitioning-big-data.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/LICENSE.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev", found 13 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/codebase-guide.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/python-api.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/CODE_OF_CONDUCT.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/guidelines-continued-dev.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/getting-started.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/for-khmer-developers.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/development.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/binary-file-formats.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/release.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/scripts-and-sandbox.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/hackathon.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/index.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/a-quick-guide-to-testing.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes", found 9 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-2.0.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.0.1.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-2.1.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.3.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.1.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/index.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.4.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.2.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.0.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/search.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/objects.inv", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/genindex.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/introduction.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/searchindex.js", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/index.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources", found 41 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/index.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/contributors.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user", found 13 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/index.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/scripts.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/choosing-table-sizes.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/galaxy.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/biblio.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/examples.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/getting-help.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/api-examples.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/blog-posts.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/guide.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/partitioning-big-data.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/known-issues.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/install.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev", found 13 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/index.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/guidelines-continued-dev.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/hackathon.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/binary-file-formats.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/release.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/python-api.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/development.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/codebase-guide.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/scripts-and-sandbox.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/CODE_OF_CONDUCT.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/getting-started.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/a-quick-guide-to-testing.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/for-khmer-developers.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes", found 9 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.4.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.1.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.0.1.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/index.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.0.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.2.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-2.0.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-2.1.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.3.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/LICENSE.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/introduction.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/roadmap.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/contributors.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.buildinfo", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/README.rst", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/run-unit-test", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/copyright", found 1 files. Now scanning "debian/khmer-common/usr/share/file", found 1 files. Now scanning "debian/khmer-common/usr/share/file/khmer", found 1 files. Now scanning "debian/khmer-common/usr/share/file/khmer/magic", found 1 files. Now have 1928 files in total. Removed 1631 files due to nonunique device and inode. Total size is 11813201 bytes or 11 MiB Removed 112 files due to unique sizes from list. 185 files left. Now eliminating candidates based on first bytes: removed 3 files from list. 182 files left. Now eliminating candidates based on last bytes: removed 0 files from list. 182 files left. Now eliminating candidates based on sha1 checksum: removed 0 files from list. 182 files left. It seems like you have 182 files that are not unique Totally, 5 MiB can be reduced. Now making results file results.txt Now making symbolic links. creating Making 91 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 -O--buildsystem=pybuild install -p -m0644 debian/changelog debian/khmer/usr/share/doc/khmer/changelog.Debian install -p -m0644 debian/changelog debian/khmer-common/usr/share/doc/khmer-common/changelog.Debian install -p -m0644 debian/changelog debian/liboxli1/usr/share/doc/liboxli1/changelog.Debian install -p -m0644 debian/changelog debian/liboxli-dev/usr/share/doc/liboxli-dev/changelog.Debian dh_installman -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 -O--buildsystem=pybuild D: dh_python3 dh_python3:175: version: 5.20220819 D: dh_python3 dh_python3:176: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:177: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, 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 khmer-common (missing ${python3:Depends} in Depends/Recommends) 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-screed', 'python3 (>= 3.2) | python3 (<< 2.6) | python3 (>> 2.7)', 'cython3', 'python3:any', 'python3 (<< 3.11)', 'python3 (>= 3.10~)'}; R=[]; S=[]; E=[], B=[]; RT=[('/usr/lib/khmer', '')] dh_installsystemduser -O--buildsystem=pybuild dh_lintian -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 -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt ln -s ../../CITATION debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.woff ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Light-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Italic-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Bold-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.svg ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Italic-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.svg rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.woff ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Regular-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.svg ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.svg rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Regular-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Light-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.svg ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Light-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.svg rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.woff ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Bold-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.svg ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.svg rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.svg ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.svg rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.woff ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Italic-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Italic-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.woff ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.svg ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.svg rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.woff ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Regular-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.svg ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.svg rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Light-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.woff ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.woff ln -s 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debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.ttf ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/glyphicons-halflings-regular.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/bootstrap.min.css ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/css/bootstrap.min.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/bootstrap.min.css rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/font-face.css ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/css/font-face.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/font-face.css rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/bootstrap-theme.min.css ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/css/bootstrap-theme.min.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/bootstrap-theme.min.css rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.js ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/js/bootstrap.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.min.js ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/js/bootstrap.min.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.min.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js ln -s ../../../../javascript/sphinxdoc/1.0/doctools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js ln -s ../../../../javascript/sphinxdoc/1.0/language_data.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js ln -s ../../../../javascript/sphinxdoc/1.0/jquery.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js ln -s ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js ln -s ../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/jquery.min.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js ln -s ../../../../javascript/sphinxdoc/1.0/underscore.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js rm -f debian/liboxli-dev/usr/lib/x86_64-linux-gnu/liboxli.so ln -s liboxli.so.1 debian/liboxli-dev/usr/lib/x86_64-linux-gnu/liboxli.so dh_strip_nondeterminism -O--buildsystem=pybuild Using 1661162028 as canonical time Normalizing debian/khmer-common/usr/share/doc/khmer-common/html/_static/file.png using File::StripNondeterminism::handlers::png Normalizing debian/khmer-common/usr/share/doc/khmer-common/html/_static/plus.png using File::StripNondeterminism::handlers::png Normalizing debian/khmer-common/usr/share/doc/khmer-common/html/_images/artifact-removal.png using File::StripNondeterminism::handlers::png Normalizing debian/khmer-common/usr/share/doc/khmer-common/html/_static/minus.png using File::StripNondeterminism::handlers::png Normalizing debian/khmer-common/usr/share/doc/khmer-common/html/_images/partitioning-workflow.png using File::StripNondeterminism::handlers::png Using 1661162028 as canonical time 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/100-reads.fq.truncated.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/test-abund-read-2.fa.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 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/test-reads.fq.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 dh_compress -O--buildsystem=pybuild cd debian/khmer-common cd debian/khmer cd debian/liboxli1 cd debian/liboxli-dev chmod a-x usr/share/doc/khmer-common/CITATION usr/share/doc/khmer-common/changelog.Debian chmod a-x usr/share/doc/khmer/changelog.Debian usr/share/man/man1/khmer.1 chmod a-x usr/share/doc/liboxli1/changelog.Debian gzip -9nf usr/share/doc/khmer-common/CITATION usr/share/doc/khmer-common/changelog.Debian gzip -9nf 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/liboxli-dev/changelog.Debian cd '/<>' cd '/<>' cd '/<>' cd '/<>' rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt.gz ln -s ../../CITATION.gz debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt.gz dh_fixperms -O--buildsystem=pybuild find debian/khmer-common ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s 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-common/usr/share/doc -type f -a -true -a ! -regex 'debian/khmer-common/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/khmer/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-common/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/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/khmer-common -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/usr/include -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/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 -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/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x 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/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dwz -- debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 install -d debian/khmer/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/khmer/usr/lib/debug/.dwz/x86_64-linux-gnu/khmer.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/khmer.debug -- debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-x86_64-linux-gnu.so objcopy --compress-debug-sections debian/khmer/usr/lib/debug/.dwz/x86_64-linux-gnu/khmer.debug dh_strip -a -O--buildsystem=pybuild debugedit --build-id --build-id-seed=liboxli1/2.1.2\+dfsg-11 debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 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/x86_64-linux-gnu/liboxli.a debugedit --build-id --build-id-seed=khmer/2.1.2\+dfsg-11 debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-x86_64-linux-gnu.so debugedit: debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 5681d56c659dafc49861c35491389d0be664527e install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/56 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/56/81d56c659dafc49861c35491389d0be664527e.debug readelf -W --section-headers debian/liboxli-dev/usr/lib/x86_64-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}' 42a37756b4de2d6143a806c126034408dcc91a9b install -d debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/42 objcopy --only-keep-debug --compress-debug-sections debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/42/a37756b4de2d6143a806c126034408dcc91a9b.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/56/81d56c659dafc49861c35491389d0be664527e.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/wDSqI8v5e9/stripYm7zw9 debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-x86_64-linux-gnu.so chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-x86_64-linux-gnu.so /tmp/wDSqI8v5e9/stripYm7zw9 cat '/tmp/wDSqI8v5e9/stripYm7zw9' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-x86_64-linux-gnu.so' chmod --reference /tmp/wDSqI8v5e9/stripYm7zw9 debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/56/81d56c659dafc49861c35491389d0be664527e.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-x86_64-linux-gnu.so /tmp/wDSqI8v5e9/objcopyxMYJyU chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-x86_64-linux-gnu.so /tmp/wDSqI8v5e9/objcopyxMYJyU chmod 0644 -- debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/42/a37756b4de2d6143a806c126034408dcc91a9b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/QRYYfwaSzf/strip1qj5Y9 debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 cat '/tmp/wDSqI8v5e9/objcopyxMYJyU' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-x86_64-linux-gnu.so' chmod --reference debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 /tmp/QRYYfwaSzf/strip1qj5Y9 chmod --reference /tmp/wDSqI8v5e9/objcopyxMYJyU debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-310-x86_64-linux-gnu.so cat '/tmp/QRYYfwaSzf/strip1qj5Y9' > 'debian/liboxli1/usr/lib/x86_64-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/assembly.cpython-310-x86_64-linux-gnu.so chmod --reference /tmp/QRYYfwaSzf/strip1qj5Y9 debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 objcopy --add-gnu-debuglink debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/42/a37756b4de2d6143a806c126034408dcc91a9b.debug debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 /tmp/QRYYfwaSzf/objcopyrE1eTC debugedit: debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 chmod --reference debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 /tmp/QRYYfwaSzf/objcopyrE1eTC cat '/tmp/QRYYfwaSzf/objcopyrE1eTC' > 'debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1' chmod --reference /tmp/QRYYfwaSzf/objcopyrE1eTC debian/liboxli1/usr/lib/x86_64-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 4861f169d9fecf38d53e0146a1283fc85ecf20ae install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/48 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/48/61f169d9fecf38d53e0146a1283fc85ecf20ae.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/48/61f169d9fecf38d53e0146a1283fc85ecf20ae.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/wDSqI8v5e9/stripktbGmo debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-x86_64-linux-gnu.so chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-x86_64-linux-gnu.so /tmp/wDSqI8v5e9/stripktbGmo cat '/tmp/wDSqI8v5e9/stripktbGmo' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-x86_64-linux-gnu.so' chmod --reference /tmp/wDSqI8v5e9/stripktbGmo debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/48/61f169d9fecf38d53e0146a1283fc85ecf20ae.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-x86_64-linux-gnu.so /tmp/wDSqI8v5e9/objcopyakGY5m chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-x86_64-linux-gnu.so /tmp/wDSqI8v5e9/objcopyakGY5m cat '/tmp/wDSqI8v5e9/objcopyakGY5m' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-x86_64-linux-gnu.so' chmod --reference /tmp/wDSqI8v5e9/objcopyakGY5m debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-x86_64-linux-gnu.so debugedit --build-id --build-id-seed=khmer/2.1.2\+dfsg-11 debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-x86_64-linux-gnu.so debugedit: debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 c8ab4cec5197e4f78119126bd3d20091c43a787e install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/c8 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/c8/ab4cec5197e4f78119126bd3d20091c43a787e.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/c8/ab4cec5197e4f78119126bd3d20091c43a787e.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/wDSqI8v5e9/strip32shU5 debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-x86_64-linux-gnu.so chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-x86_64-linux-gnu.so /tmp/wDSqI8v5e9/strip32shU5 cat '/tmp/wDSqI8v5e9/strip32shU5' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-x86_64-linux-gnu.so' chmod --reference /tmp/wDSqI8v5e9/strip32shU5 debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/c8/ab4cec5197e4f78119126bd3d20091c43a787e.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-x86_64-linux-gnu.so /tmp/wDSqI8v5e9/objcopyqWEucD chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-x86_64-linux-gnu.so /tmp/wDSqI8v5e9/objcopyqWEucD cat '/tmp/wDSqI8v5e9/objcopyqWEucD' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-x86_64-linux-gnu.so' chmod --reference /tmp/wDSqI8v5e9/objcopyqWEucD debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-x86_64-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-x86_64-linux-gnu.so debugedit: debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 843bc979c28827caa0344dfaadb6ba388917026a install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/84 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/84/3bc979c28827caa0344dfaadb6ba388917026a.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/84/3bc979c28827caa0344dfaadb6ba388917026a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/wDSqI8v5e9/stripWZJVy3 debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-x86_64-linux-gnu.so chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-x86_64-linux-gnu.so /tmp/wDSqI8v5e9/stripWZJVy3 cat '/tmp/wDSqI8v5e9/stripWZJVy3' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-x86_64-linux-gnu.so' chmod --reference /tmp/wDSqI8v5e9/stripWZJVy3 debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/84/3bc979c28827caa0344dfaadb6ba388917026a.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-x86_64-linux-gnu.so /tmp/wDSqI8v5e9/objcopyzVI8VP chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-x86_64-linux-gnu.so /tmp/wDSqI8v5e9/objcopyzVI8VP cat '/tmp/wDSqI8v5e9/objcopyzVI8VP' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-x86_64-linux-gnu.so' chmod --reference /tmp/wDSqI8v5e9/objcopyzVI8VP debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-x86_64-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-x86_64-linux-gnu.so debugedit: debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 301a5f3a387aa3d33841fc05c5022213507dd308 install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/30 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/30/1a5f3a387aa3d33841fc05c5022213507dd308.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/30/1a5f3a387aa3d33841fc05c5022213507dd308.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/wDSqI8v5e9/stripDrrPLn debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-x86_64-linux-gnu.so chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-x86_64-linux-gnu.so /tmp/wDSqI8v5e9/stripDrrPLn cat '/tmp/wDSqI8v5e9/stripDrrPLn' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-x86_64-linux-gnu.so' chmod --reference /tmp/wDSqI8v5e9/stripDrrPLn debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/30/1a5f3a387aa3d33841fc05c5022213507dd308.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-x86_64-linux-gnu.so /tmp/wDSqI8v5e9/objcopyQ9YvLt chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-x86_64-linux-gnu.so /tmp/wDSqI8v5e9/objcopyQ9YvLt cat '/tmp/wDSqI8v5e9/objcopyQ9YvLt' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-x86_64-linux-gnu.so' chmod --reference /tmp/wDSqI8v5e9/objcopyQ9YvLt debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-x86_64-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-x86_64-linux-gnu.so debugedit: debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 e603c914b21d318d4566d9103005b7ddfee32fe5 install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/e6 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/e6/03c914b21d318d4566d9103005b7ddfee32fe5.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/e6/03c914b21d318d4566d9103005b7ddfee32fe5.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/wDSqI8v5e9/stripuulTGT debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-x86_64-linux-gnu.so chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-x86_64-linux-gnu.so /tmp/wDSqI8v5e9/stripuulTGT cat '/tmp/wDSqI8v5e9/stripuulTGT' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-x86_64-linux-gnu.so' chmod --reference /tmp/wDSqI8v5e9/stripuulTGT debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/e6/03c914b21d318d4566d9103005b7ddfee32fe5.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-x86_64-linux-gnu.so /tmp/wDSqI8v5e9/objcopyxUr8NS chmod --reference debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-x86_64-linux-gnu.so /tmp/wDSqI8v5e9/objcopyxUr8NS cat '/tmp/wDSqI8v5e9/objcopyxUr8NS' > 'debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-x86_64-linux-gnu.so' chmod --reference /tmp/wDSqI8v5e9/objcopyxUr8NS debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-x86_64-linux-gnu.so install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/khmer/usr/lib/debug/.dwz/x86_64-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/x86_64-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-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-310-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-310-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-310-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-310-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-310-x86_64-linux-gnu.so dpkg-shlibdeps: warning: symbol gzeof used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol inflate used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol inflateInit2_ used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol deflateEnd used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol crc32 used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzdirect used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzwrite used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol BZ2_bzReadClose used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol BZ2_bzRead used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gztell64 used by debian/liboxli1/usr/lib/x86_64-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 -O--buildsystem=pybuild install -d debian/khmer-common/DEBIAN cp -f debian/khmer-common.postinst debian/khmer-common/DEBIAN/postinst [META] Replace #TOKEN#s in "debian/khmer-common/DEBIAN/postinst" chmod 0755 -- debian/khmer-common/DEBIAN/postinst cp -f debian/khmer-common.postrm debian/khmer-common/DEBIAN/postrm [META] Replace #TOKEN#s in "debian/khmer-common/DEBIAN/postrm" chmod 0755 -- debian/khmer-common/DEBIAN/postrm 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 -O--buildsystem=pybuild echo misc:Depends= >> debian/khmer-common.substvars echo misc:Pre-Depends= >> debian/khmer-common.substvars dpkg-gencontrol -pkhmer-common -ldebian/changelog -Tdebian/khmer-common.substvars -Pdebian/khmer-common 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=301a5f3a387aa3d33841fc05c5022213507dd308 4861f169d9fecf38d53e0146a1283fc85ecf20ae 5681d56c659dafc49861c35491389d0be664527e 843bc979c28827caa0344dfaadb6ba388917026a c8ab4cec5197e4f78119126bd3d20091c43a787e e603c914b21d318d4566d9103005b7ddfee32fe5" -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=42a37756b4de2d6143a806c126034408dcc91a9b -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/khmer-common/DEBIAN/control chmod 0644 -- debian/liboxli1/DEBIAN/control chmod 0644 -- debian/khmer/DEBIAN/control dh_md5sums -O--buildsystem=pybuild cd debian/liboxli-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums 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/khmer-common >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/liboxli1/DEBIAN/md5sums chmod 0644 -- debian/liboxli-dev/DEBIAN/md5sums cd debian/.debhelper/liboxli1/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/khmer-common/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 -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/khmer-common .. 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 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 INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing khmer-common (in debian/khmer-common); do_strip: , oemstrip: pkgstriptranslations: processing khmer-dbgsym (in debian/.debhelper/khmer/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing liboxli1-dbgsym (in debian/.debhelper/liboxli1/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/khmer-common/DEBIAN/control, package khmer-common, directory debian/khmer-common 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_amd64.deb'. pkgstripfiles: Truncating usr/share/doc/khmer-common/changelog.Debian.gz to topmost ten records 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_amd64.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package khmer-common ... xargs: warning: options --max-lines and --replace/-I/-i are mutually exclusive, ignoring previous --max-lines value ...oo pkgstripfiles: PNG optimization (2/0) for package khmer-common took 0 s dpkg-deb: building package 'khmer-common' in '../khmer-common_2.1.2+dfsg-11_all.deb'. Renaming liboxli1-dbgsym_2.1.2+dfsg-11_amd64.deb to liboxli1-dbgsym_2.1.2+dfsg-11_amd64.ddeb mv debian/.debhelper/scratch-space/build-liboxli1/liboxli1-dbgsym_2.1.2\+dfsg-11_amd64.deb ../liboxli1-dbgsym_2.1.2\+dfsg-11_amd64.ddeb dpkg-deb --root-owner-group --build debian/liboxli-dev .. INFO: pkgstriptranslations version 149 pkgstriptranslations: processing liboxli-dev (in debian/liboxli-dev); do_strip: , oemstrip: 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) ... dpkg-deb --root-owner-group --build debian/khmer .. INFO: pkgstriptranslations version 149 pkgstriptranslations: processing khmer (in debian/khmer); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/khmer/DEBIAN/control, package khmer, directory debian/khmer Skipping arch: any to arch: all dependency to khmer-common 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_amd64.deb'. INFO: pkgstripfiles: waiting for lock (liboxli-dev) ... INFO: pkgstripfiles: waiting for lock (liboxli-dev) ... INFO: pkgstripfiles: waiting for lock (liboxli-dev) ... Renaming khmer-dbgsym_2.1.2+dfsg-11_amd64.deb to khmer-dbgsym_2.1.2+dfsg-11_amd64.ddeb mv debian/.debhelper/scratch-space/build-khmer/khmer-dbgsym_2.1.2\+dfsg-11_amd64.deb ../khmer-dbgsym_2.1.2\+dfsg-11_amd64.ddeb dpkg-deb --root-owner-group --build debian/liboxli1 .. INFO: pkgstriptranslations version 149 pkgstriptranslations: processing liboxli1 (in debian/liboxli1); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/liboxli1/DEBIAN/control, package liboxli1, directory debian/liboxli1 Skipping arch: any to arch: all dependency to khmer-common pkgstripfiles: Truncating usr/share/doc/liboxli1/changelog.Debian.gz to topmost ten records 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_amd64.deb'. Searching for duplicated docs in dependency liboxli1... symlinking changelog.Debian.gz in liboxli-dev to file in liboxli1 Skipping arch: any to arch: all dependency to khmer-common 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_amd64.deb'. dpkg-genbuildinfo --build=binary -O../khmer_2.1.2+dfsg-11_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../khmer_2.1.2+dfsg-11_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-08-22T17:26:07Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ khmer_2.1.2+dfsg-11_amd64.changes: ---------------------------------- Format: 1.8 Date: Mon, 22 Aug 2022 11:53:48 +0200 Source: khmer Binary: khmer khmer-common liboxli-dev liboxli1 Built-For-Profiles: noudeb Architecture: all amd64 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 khmer-common - common files for the khmer project tools 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: 682f660f4473a0908f00443fc433a1cd4a573138 191794 khmer-common_2.1.2+dfsg-11_all.deb 29590ff330f4fee3a06caf35be962e12c4602fd0 15431678 khmer-dbgsym_2.1.2+dfsg-11_amd64.ddeb d885a5b4f8c9f3d58f87a2bb9c4b76070bc5abbd 10537 khmer_2.1.2+dfsg-11_amd64.buildinfo df0d44f355e252e5ed5fc792cbaaeb0cc6b0f3f3 6869522 khmer_2.1.2+dfsg-11_amd64.deb 70e1f865794297b1d588e3bad2fa837836cc98c9 309104 liboxli-dev_2.1.2+dfsg-11_amd64.deb fad6a23325aa17e37a88634cd3dae759284d9c35 2222008 liboxli1-dbgsym_2.1.2+dfsg-11_amd64.ddeb 580b23a4c80e8a9447b268b0d858a9a834e7738d 216566 liboxli1_2.1.2+dfsg-11_amd64.deb Checksums-Sha256: e423d4378716ca43f64fa469acc46db5daf43b542e466a2944f924df0fe7b125 191794 khmer-common_2.1.2+dfsg-11_all.deb 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khmer_2.1.2+dfsg-11_amd64.deb 9a89d4a8611d696f73345c95921ff510 309104 libdevel optional liboxli-dev_2.1.2+dfsg-11_amd64.deb b0824d4d8fa265468122a36f6e5458a5 2222008 debug optional liboxli1-dbgsym_2.1.2+dfsg-11_amd64.ddeb a168b6ad5e12b90a43c824c35f7e35ae 216566 libs optional liboxli1_2.1.2+dfsg-11_amd64.deb /<>/khmer_2.1.2+dfsg-11_amd64.changes.new could not be renamed to /<>/khmer_2.1.2+dfsg-11_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: khmer Binary: khmer khmer-common khmer-dbgsym liboxli-dev liboxli1 liboxli1-dbgsym Architecture: all amd64 Version: 2.1.2+dfsg-11 Checksums-Md5: 3404b51b3dbd8daab65586bcb430b531 191794 khmer-common_2.1.2+dfsg-11_all.deb a699ddcebe07e3c99d58f3ed87e33a23 15431678 khmer-dbgsym_2.1.2+dfsg-11_amd64.ddeb c1d6f161914ad4597bbd1b45f06bd989 6869522 khmer_2.1.2+dfsg-11_amd64.deb 9a89d4a8611d696f73345c95921ff510 309104 liboxli-dev_2.1.2+dfsg-11_amd64.deb b0824d4d8fa265468122a36f6e5458a5 2222008 liboxli1-dbgsym_2.1.2+dfsg-11_amd64.ddeb a168b6ad5e12b90a43c824c35f7e35ae 216566 liboxli1_2.1.2+dfsg-11_amd64.deb Checksums-Sha1: 682f660f4473a0908f00443fc433a1cd4a573138 191794 khmer-common_2.1.2+dfsg-11_all.deb 29590ff330f4fee3a06caf35be962e12c4602fd0 15431678 khmer-dbgsym_2.1.2+dfsg-11_amd64.ddeb df0d44f355e252e5ed5fc792cbaaeb0cc6b0f3f3 6869522 khmer_2.1.2+dfsg-11_amd64.deb 70e1f865794297b1d588e3bad2fa837836cc98c9 309104 liboxli-dev_2.1.2+dfsg-11_amd64.deb fad6a23325aa17e37a88634cd3dae759284d9c35 2222008 liboxli1-dbgsym_2.1.2+dfsg-11_amd64.ddeb 580b23a4c80e8a9447b268b0d858a9a834e7738d 216566 liboxli1_2.1.2+dfsg-11_amd64.deb Checksums-Sha256: e423d4378716ca43f64fa469acc46db5daf43b542e466a2944f924df0fe7b125 191794 khmer-common_2.1.2+dfsg-11_all.deb 4de8799d13bfed69faa30207e21a3eaa0b4c2acd9e1ff21b9f089ca44feaf9fe 15431678 khmer-dbgsym_2.1.2+dfsg-11_amd64.ddeb 8466b122917404abf99e956bf906f2664fcb9d5fd29847bf36267e8515ab55bb 6869522 khmer_2.1.2+dfsg-11_amd64.deb dfaf18262eb6491a7843d306c5cf2d7bd9ea0f1009aadb381a6957673571292c 309104 liboxli-dev_2.1.2+dfsg-11_amd64.deb e04e3ea74b9f565e7bfc1998fceebfe03a04bae904306cf71d7355c094701f02 2222008 liboxli1-dbgsym_2.1.2+dfsg-11_amd64.ddeb f5357f048bde4b039520adf2456e550fddf9e16b4077c621a4d9f44bada6af8e 216566 liboxli1_2.1.2+dfsg-11_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Mon, 22 Aug 2022 17:26:06 +0000 Build-Path: /<> 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-common (= 2.39-1ubuntu1), binutils-x86-64-linux-gnu (= 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 (= 12.2.0-1ubuntu1), 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), 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++-12 (= 12.2.0-1ubuntu1), gcc (= 4:12.1.0-3ubuntu1), gcc-11 (= 11.3.0-5ubuntu1), gcc-11-base (= 11.3.0-5ubuntu1), gcc-12 (= 12.2.0-1ubuntu1), gcc-12-base (= 12.2.0-1ubuntu1), gettext (= 0.21-8), gettext-base (= 0.21-8), grep (= 3.7-1build1), groff-base (= 1.22.4-8build1), gzip (= 1.12-1ubuntu1), hostname (= 3.23ubuntu2), init-system-helpers (= 1.64), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libapparmor1 (= 3.0.7-1ubuntu1), libarchive-zip-perl (= 1.68-1), libargon2-1 (= 0~20171227-0.3), libasan6 (= 11.3.0-5ubuntu1), libasan8 (= 12.2.0-1ubuntu1), libatomic1 (= 12.2.0-1ubuntu1), 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 (= 12.2.0-1ubuntu1), 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), 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 (= 12.2.0-1ubuntu1), libgcc-s1 (= 12.2.0-1ubuntu1), libgcrypt20 (= 1.10.1-2ubuntu1), libgdbm-compat4 (= 1.23-1), libgdbm6 (= 1.23-1), libgmp10 (= 2:6.2.1+dfsg-3ubuntu1), libgomp1 (= 12.2.0-1ubuntu1), libgpg-error0 (= 1.45-2), libgprofng0 (= 2.39-1ubuntu1), libgssapi-krb5-2 (= 1.20-1), libicu71 (= 71.1-3), libip4tc2 (= 1.8.7-1ubuntu6), libisl23 (= 0.25-1), libitm1 (= 12.2.0-1ubuntu1), libjs-bootstrap (= 3.4.1+dfsg-2), libjs-jquery (= 3.6.0+dfsg+~3.5.13-1), libjs-sphinxdoc (= 4.5.0-4), libjs-underscore (= 1.13.3~dfsg+~1.11.4-1), libjson-c5 (= 0.16-1), libjson-perl (= 4.09000-1), libk5crypto3 (= 1.20-1), libkeyutils1 (= 1.6.3-1), libkmod2 (= 30+20220630-3ubuntu1), libkrb5-3 (= 1.20-1), libkrb5support0 (= 1.20-1), liblsan0 (= 12.2.0-1ubuntu1), liblz4-1 (= 1.9.3-2build2), liblzma5 (= 5.2.5-2.1), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmd0 (= 1.0.4-2), libmount1 (= 2.38-4ubuntu1), libmpc3 (= 1.2.1-2build1), libmpdec3 (= 2.5.1-2build2), libmpfr6 (= 4.1.0-3build3), libncurses6 (= 6.3+20220423-2), libncursesw6 (= 6.3+20220423-2), libnettle8 (= 3.8.1-2), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libpam-modules (= 1.5.2-2ubuntu1), libpam-modules-bin (= 1.5.2-2ubuntu1), libpam-runtime (= 1.5.2-2ubuntu1), libpam0g (= 1.5.2-2ubuntu1), libpcre2-8-0 (= 10.40-1), libpcre3 (= 2:8.39-14), libperl5.34 (= 5.34.0-5ubuntu1), libpipeline1 (= 1.5.6-2), 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), libquadmath0 (= 12.2.0-1ubuntu1), 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 (= 2.14-1ubuntu1), libsmartcols1 (= 2.38-4ubuntu1), libsqlite3-0 (= 3.39.2-1), libssl3 (= 3.0.5-2ubuntu1), libstdc++-12-dev (= 12.2.0-1ubuntu1), libstdc++6 (= 12.2.0-1ubuntu1), libsub-override-perl (= 0.09-3), libsystemd0 (= 251.2-2ubuntu2), 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 (= 12.2.0-1ubuntu1), libubsan1 (= 12.2.0-1ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 251.2-2ubuntu2), libunistring2 (= 1.0-1), libuuid1 (= 2.38-4ubuntu1), libxml2 (= 2.9.14+dfsg-1), libyaml-0-2 (= 0.2.5-1), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.19.0-15.15), login (= 1:4.11.1+dfsg1-2ubuntu1), 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), 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), po-debconf (= 1.0.21+nmu1), 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), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), sgml-base (= 1.30), sphinx-common (= 4.5.0-4), systemd (= 251.2-2ubuntu2), sysvinit-utils (= 3.01-1ubuntu1), tar (= 1.34+dfsg-1build3), tzdata (= 2022a-0ubuntu1), 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) 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-common_2.1.2+dfsg-11_all.deb ---------------------------------- new Debian package, version 2.0. size 191794 bytes: control archive=3664 bytes. 835 bytes, 20 lines control 9670 bytes, 105 lines md5sums 60 bytes, 3 lines * postinst #!/bin/sh 46 bytes, 3 lines * postrm #!/bin/sh Package: khmer-common Source: khmer Version: 2.1.2+dfsg-11 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1604 Depends: file, libjs-sphinxdoc (>= 4.3), python3-guzzle-sphinx-theme Built-Using: sphinx (= 4.5.0-4) Section: science Priority: optional Multi-Arch: foreign Homepage: https://khmer.readthedocs.org Description: common files for the khmer project tools 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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../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Italic-webfont.ttf lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.woff -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Italic-webfont.woff lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.eot -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Light-webfont.eot lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.svg -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Light-webfont.svg lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.ttf -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Light-webfont.ttf lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.woff -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Light-webfont.woff lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.eot -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.eot lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.svg -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.svg lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.ttf -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.ttf lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.woff -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.woff lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.eot -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Regular-webfont.eot lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.svg -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Regular-webfont.svg lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.ttf -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Regular-webfont.ttf lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.woff -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Regular-webfont.woff lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.eot -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.eot lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.svg -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.svg lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.ttf -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.ttf lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.woff -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.woff lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.eot -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.eot lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.svg -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.svg lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.ttf -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.ttf lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.woff -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.woff lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/open-sans/stylesheet.css -> ../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/stylesheet.css drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/ drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/ lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Black.eot -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/EOT/SourceSerifPro-Black.eot lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Bold.eot -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/EOT/SourceSerifPro-Bold.eot lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-ExtraLight.eot -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/EOT/SourceSerifPro-ExtraLight.eot lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Light.eot -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/EOT/SourceSerifPro-Light.eot lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Regular.eot -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/EOT/SourceSerifPro-Regular.eot lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Semibold.eot -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/EOT/SourceSerifPro-Semibold.eot drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/ lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Black.otf -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/OTF/SourceSerifPro-Black.otf lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Bold.otf -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/OTF/SourceSerifPro-Bold.otf lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-ExtraLight.otf -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/OTF/SourceSerifPro-ExtraLight.otf lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Light.otf -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/OTF/SourceSerifPro-Light.otf lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Regular.otf -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/OTF/SourceSerifPro-Regular.otf lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Semibold.otf -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/OTF/SourceSerifPro-Semibold.otf lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/README.md -> ../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README.md lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/ReadMe.html -> ../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/ReadMe.html lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/SourceSerifProReadMe.html -> ../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/SourceSerifProReadMe.html drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/ lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Black.ttf -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/TTF/SourceSerifPro-Black.ttf lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Bold.ttf -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/TTF/SourceSerifPro-Bold.ttf lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-ExtraLight.ttf -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/TTF/SourceSerifPro-ExtraLight.ttf lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Light.ttf -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/TTF/SourceSerifPro-Light.ttf lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Regular.ttf -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/TTF/SourceSerifPro-Regular.ttf lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Semibold.ttf -> ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/TTF/SourceSerifPro-Semibold.ttf drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/ drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/ lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Black.otf.woff -> ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Black.otf.woff lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Bold.otf.woff -> ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Bold.otf.woff lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-ExtraLight.otf.woff -> 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../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Semibold.otf.woff drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/ lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Black.ttf.woff -> ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Black.ttf.woff lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Bold.ttf.woff -> ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Bold.ttf.woff lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-ExtraLight.ttf.woff -> ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-ExtraLight.ttf.woff lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Light.ttf.woff -> ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Light.ttf.woff lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Regular.ttf.woff -> ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Regular.ttf.woff lrwxrwxrwx root/root 0 2022-08-22 09:53 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2.0. size 6869522 bytes: control archive=7056 bytes. 890 bytes, 16 lines control 22225 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: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 29213 Depends: khmer-common, python3 (<< 3.11), python3-screed, libbz2-1.0, libc6 (>= 2.32), libgcc-s1 (>= 3.4), 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. 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./usr/share/python3/runtime.d/khmer.rtupdate liboxli-dev_2.1.2+dfsg-11_amd64.deb ----------------------------------- new Debian package, version 2.0. size 309104 bytes: control archive=1244 bytes. 805 bytes, 19 lines control 1255 bytes, 19 lines md5sums Package: liboxli-dev Source: khmer Version: 2.1.2+dfsg-11 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1522 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. . This package contains the low-level C++ library headers and static archive. 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/include/ drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/include/oxli/ -rw-r--r-- root/root 1960 2017-07-03 12:55 ./usr/include/oxli/alphabets.hh -rw-r--r-- root/root 5783 2017-07-03 12:55 ./usr/include/oxli/assembler.hh -rw-r--r-- root/root 8760 2017-07-03 12:55 ./usr/include/oxli/hashgraph.hh -rw-r--r-- root/root 13471 2017-07-03 12:55 ./usr/include/oxli/hashtable.hh -rw-r--r-- root/root 76379 2017-07-03 12:55 ./usr/include/oxli/hllcounter.hh -rw-r--r-- root/root 2482 2017-07-03 12:55 ./usr/include/oxli/kmer_filters.hh -rw-r--r-- root/root 12255 2017-07-03 12:55 ./usr/include/oxli/kmer_hash.hh -rw-r--r-- root/root 6960 2017-07-03 12:55 ./usr/include/oxli/labelhash.hh -rw-r--r-- root/root 5745 2017-07-03 12:55 ./usr/include/oxli/oxli.hh -rw-r--r-- root/root 3905 2017-07-03 12:55 ./usr/include/oxli/oxli_exception.hh -rw-r--r-- root/root 9447 2017-07-03 12:55 ./usr/include/oxli/read_aligner.hh -rw-r--r-- root/root 6444 2017-07-03 12:55 ./usr/include/oxli/read_parsers.hh drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/include/oxli/smhasher/ -rw-r--r-- root/root 960 2017-07-03 12:55 ./usr/include/oxli/smhasher/MurmurHash3.h -rw-r--r-- root/root 19333 2017-07-03 12:55 ./usr/include/oxli/storage.hh -rw-r--r-- root/root 6408 2017-07-03 12:55 ./usr/include/oxli/subset.hh -rw-r--r-- root/root 8205 2017-07-03 12:55 ./usr/include/oxli/traversal.hh 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/x86_64-linux-gnu/ -rw-r--r-- root/root 1340390 2022-08-22 09:53 ./usr/lib/x86_64-linux-gnu/liboxli.a lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/lib/x86_64-linux-gnu/liboxli.so -> liboxli.so.1 drwxr-xr-x root/root 0 2022-08-22 09:53 ./usr/lib/x86_64-linux-gnu/pkgconfig/ -rw-r--r-- root/root 364 2022-08-22 09:53 ./usr/lib/x86_64-linux-gnu/pkgconfig/oxli.pc 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/liboxli-dev/ lrwxrwxrwx root/root 0 2022-08-22 09:53 ./usr/share/doc/liboxli-dev/changelog.Debian.gz -> ../liboxli1/changelog.Debian.gz -rw-r--r-- root/root 4466 2022-08-22 09:53 ./usr/share/doc/liboxli-dev/copyright liboxli1_2.1.2+dfsg-11_amd64.deb -------------------------------- new Debian package, version 2.0. size 216566 bytes: control archive=921 bytes. 837 bytes, 19 lines control 287 bytes, 4 lines md5sums 35 bytes, 1 lines shlibs 72 bytes, 2 lines triggers Package: liboxli1 Source: khmer Version: 2.1.2+dfsg-11 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 552 Depends: khmer-common, libc6 (>= 2.32), libgcc-s1 (>= 3.4), libgomp1 (>= 4.9), libstdc++6 (>= 11) Section: libs Priority: optional Multi-Arch: same Homepage: https://khmer.readthedocs.org Description: in-memory DNA sequence analysis library from the khmer project 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. . 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/x86_64-linux-gnu/ -rw-r--r-- root/root 542936 2022-08-22 09:53 ./usr/lib/x86_64-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: amd64 Build Type: binary Build-Space: 541440 Build-Time: 414 Distribution: kinetic-proposed Host Architecture: amd64 Install-Time: 16 Job: khmer_2.1.2+dfsg-11.dsc Machine Architecture: amd64 Package: khmer Package-Time: 431 Source-Version: 2.1.2+dfsg-11 Space: 541440 Status: successful Version: 2.1.2+dfsg-11 -------------------------------------------------------------------------------- Finished at 2022-08-22T17:26:07Z Build needed 00:07:11, 541440k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24304738 Scanning for processes to kill in build PACKAGEBUILD-24304738