I: pbuilder: network access will be disabled during build I: Current time: Thu Jun 8 00:12:51 +14 2023 I: pbuilder-time-stamp: 1686132771 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [khmer_3.0.0~a3+dfsg-4.dsc] I: copying [./khmer_3.0.0~a3+dfsg.orig.tar.xz] I: copying [./khmer_3.0.0~a3+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Sep 25 05:47:53 2022 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./khmer_3.0.0~a3+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting khmer in khmer-3.0.0~a3+dfsg dpkg-source: info: unpacking khmer_3.0.0~a3+dfsg.orig.tar.xz dpkg-source: info: unpacking khmer_3.0.0~a3+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_non_x86_build dpkg-source: info: applying hardening 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 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 dpkg-source: info: applying refresh_cython dpkg-source: info: applying find_object_files_at_right_loc.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3152983/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 8 00:13 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3152983/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3152983/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=961fc50462764d7996f45764041fdd48 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3152983 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.OjVxdJVv/pbuilderrc_CS1e --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OjVxdJVv/b2 --logfile b2/build.log --extrapackages usrmerge khmer_3.0.0~a3+dfsg-4.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 24 11:23 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash -rwxr-xr-x 1 root root 121904 Sep 21 2022 date -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd -rwxr-xr-x 1 root root 102200 Sep 21 2022 df -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 11:23 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 Jun 8 00:13 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch -rwxr-xr-x 1 root root 35664 Sep 21 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/3152983/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. 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 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19591 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on python3-guzzle-sphinx-theme; however: Package python3-guzzle-sphinx-theme is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-screed; however: Package python3-screed is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-runner; however: Package python3-pytest-runner is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.autoprogram; however: Package python3-sphinxcontrib.autoprogram is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor is not installed. pbuilder-satisfydepends-dummy depends on rdfind; however: Package rdfind is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fonts-glyphicons-halflings{a} fonts-liberation{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libbz2-dev{a} libdebhelper-perl{a} libedit2{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libicu72{a} libjs-bootstrap{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libruby{a} libruby3.1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} openssl{a} po-debconf{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-attr{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-dev{a} python3-distutils{a} python3-docutils{a} python3-guzzle-sphinx-theme{a} python3-idna{a} python3-imagesize{a} python3-iniconfig{a} python3-jinja2{a} python3-lib2to3{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-py{a} python3-pygments{a} python3-pytest{a} python3-pytest-runner{a} python3-requests{a} python3-roman{a} python3-screed{a} python3-setuptools{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinxcontrib.autoprogram{a} python3-tz{a} python3-urllib3{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} rake{a} rdfind{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} sensible-utils{a} sgml-base{a} sphinx-common{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl fonts-lato javascript-common libarchive-cpio-perl libgpm2 libjson-xs-perl libltdl-dev libmail-sendmail-perl libpaper-utils lynx python3-pil wget zip 0 packages upgraded, 120 newly installed, 0 to remove and 0 not upgraded. Need to get 57.0 MB of archives. After unpacking 237 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.9-1 [1416 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 rubygems-integration all 1.18 [6704 B] Get: 26 http://deb.debian.org/debian bookworm/main amd64 rake all 13.0.6-3 [83.9 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libruby amd64 1:3.1 [4972 B] Get: 31 http://deb.debian.org/debian bookworm/main amd64 ruby-sdbm amd64 1.0.0-5+b1 [15.4 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-4 [103 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libruby3.1 amd64 3.1.2-7 [5401 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 ruby3.1 amd64 3.1.2-7 [663 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 ruby-rubygems all 3.3.15-2 [293 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 ruby amd64 1:3.1 [5868 B] Get: 40 http://deb.debian.org/debian bookworm/main amd64 ruby-asciidoctor all 2.0.18-2 [211 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 asciidoctor all 2.0.18-2 [86.6 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 cython3 amd64 0.29.32-2+b1 [1302 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 dh-exec amd64 0.27 [27.8 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 docutils-common all 0.19+dfsg-6 [127 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 fonts-liberation all 1:1.07.4-11 [828 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libbz2-dev amd64 1.0.8-5+b1 [30.9 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6 [1988 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6 [4738 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libpython3-all-dev amd64 3.11.2-1+b1 [1068 B] Get: 83 http://deb.debian.org/debian bookworm/main amd64 python-babel-localedata all 2.10.3-1 [5615 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Get: 86 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6 [615 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 python3-all-dev amd64 3.11.2-1+b1 [1072 B] Get: 89 http://deb.debian.org/debian bookworm/main amd64 python3-attr all 22.2.0-1 [65.4 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-4 [30.1 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 python3-babel all 2.10.3-1 [103 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 python3-certifi all 2022.9.24-1 [153 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 python3-chardet all 5.1.0+dfsg-2 [110 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 python3-roman all 3.3-3 [9880 B] Get: 97 http://deb.debian.org/debian bookworm/main amd64 python3-docutils all 0.19+dfsg-6 [382 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 sphinx-common all 5.3.0-4 [653 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 100 http://deb.debian.org/debian bookworm/main amd64 python3-markupsafe amd64 2.1.2-1+b1 [13.2 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 python3-jinja2 all 3.1.2-1 [119 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 python3-pygments all 2.14.0+dfsg-1 [783 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 python3-idna all 3.3-1 [39.4 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 python3-urllib3 all 1.26.12-1 [117 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 python3-snowballstemmer all 2.2.0-2 [57.8 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 python3-sphinx all 5.3.0-4 [549 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 python3-guzzle-sphinx-theme all 0.7.11-6 [1346 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 112 http://deb.debian.org/debian bookworm/main amd64 python3-more-itertools all 8.10.0-2 [53.0 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 python3-pluggy all 1.0.0+repack-1 [19.7 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 python3-py all 1.11.0-1 [89.2 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 python3-pytest all 7.2.1-2 [236 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 python3-pytest-runner all 2.11.1-4 [8432 B] Get: 118 http://deb.debian.org/debian bookworm/main amd64 python3-screed all 1.0.5-4 [109 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 python3-sphinxcontrib.autoprogram all 0.1.7-4 [10.3 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 rdfind amd64 1.5.0-1.1+b1 [41.3 kB] Fetched 57.0 MB in 1s (41.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19591 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19907 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20341 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.0.9-1_amd64.deb ... Unpacking openssl (3.0.9-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../006-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../009-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../012-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../014-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package rake. Preparing to unpack .../015-rake_13.0.6-3_all.deb ... Unpacking rake (13.0.6-3) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../016-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../017-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../018-ruby-xmlrpc_0.3.2-2_all.deb ... Unpacking ruby-xmlrpc (0.3.2-2) ... Selecting previously unselected package libruby:amd64. Preparing to unpack .../019-libruby_1%3a3.1_amd64.deb ... Unpacking libruby:amd64 (1:3.1) ... Selecting previously unselected package ruby-sdbm:amd64. Preparing to unpack .../020-ruby-sdbm_1.0.0-5+b1_amd64.deb ... Unpacking ruby-sdbm:amd64 (1.0.0-5+b1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../021-libbsd0_0.11.7-2_amd64.deb ... Unpacking libbsd0:amd64 (0.11.7-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../022-libedit2_3.1-20221030-2_amd64.deb ... Unpacking libedit2:amd64 (3.1-20221030-2) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../023-libncurses6_6.4-4_amd64.deb ... Unpacking libncurses6:amd64 (6.4-4) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../024-libyaml-0-2_0.2.5-1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-1) ... Selecting previously unselected package libruby3.1:amd64. Preparing to unpack .../025-libruby3.1_3.1.2-7_amd64.deb ... Unpacking libruby3.1:amd64 (3.1.2-7) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../026-ruby3.1_3.1.2-7_amd64.deb ... Unpacking ruby3.1 (3.1.2-7) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../027-ruby-rubygems_3.3.15-2_all.deb ... Unpacking ruby-rubygems (3.3.15-2) ... Selecting previously unselected package ruby. Preparing to unpack .../028-ruby_1%3a3.1_amd64.deb ... Unpacking ruby (1:3.1) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../029-ruby-asciidoctor_2.0.18-2_all.deb ... Unpacking ruby-asciidoctor (2.0.18-2) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../030-asciidoctor_2.0.18-2_all.deb ... Unpacking asciidoctor (2.0.18-2) ... Selecting previously unselected package m4. Preparing to unpack .../031-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../032-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../033-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../034-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../035-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package cython3. Preparing to unpack .../036-cython3_0.29.32-2+b1_amd64.deb ... Unpacking cython3 (0.29.32-2+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../037-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../038-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../039-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../040-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../041-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../042-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../043-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../044-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../045-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../046-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../047-libxml2_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../048-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../049-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../050-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../051-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package dh-exec. Preparing to unpack .../052-dh-exec_0.27_amd64.deb ... Unpacking dh-exec (0.27) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../053-python3-lib2to3_3.11.2-3_all.deb ... Unpacking python3-lib2to3 (3.11.2-3) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../054-python3-distutils_3.11.2-3_all.deb ... Unpacking python3-distutils (3.11.2-3) ... Selecting previously unselected package dh-python. Preparing to unpack .../055-dh-python_5.20230130_all.deb ... Unpacking dh-python (5.20230130) ... Selecting previously unselected package xml-core. Preparing to unpack .../056-xml-core_0.18+nmu1_all.deb ... Unpacking xml-core (0.18+nmu1) ... Selecting previously unselected package docutils-common. Preparing to unpack .../057-docutils-common_0.19+dfsg-6_all.deb ... Unpacking docutils-common (0.19+dfsg-6) ... Selecting previously unselected package fonts-glyphicons-halflings. Preparing to unpack .../058-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Selecting previously unselected package fonts-liberation. Preparing to unpack .../059-fonts-liberation_1%3a1.07.4-11_all.deb ... Unpacking fonts-liberation (1:1.07.4-11) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../060-libbz2-dev_1.0.8-5+b1_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.8-5+b1) ... Selecting previously unselected package libexpat1-dev:amd64. Preparing to unpack .../061-libexpat1-dev_2.5.0-1_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.5.0-1) ... Selecting previously unselected package libjs-bootstrap. Preparing to unpack .../062-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../063-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../064-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../065-libjs-sphinxdoc_5.3.0-4_all.deb ... Unpacking libjs-sphinxdoc (5.3.0-4) ... Selecting previously unselected package libjson-perl. Preparing to unpack .../066-libjson-perl_4.10000-1_all.deb ... Unpacking libjson-perl (4.10000-1) ... Selecting previously unselected package libpython3.11:amd64. Preparing to unpack .../067-libpython3.11_3.11.2-6_amd64.deb ... Unpacking libpython3.11:amd64 (3.11.2-6) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../068-zlib1g-dev_1%3a1.2.13.dfsg-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Selecting previously unselected package libpython3.11-dev:amd64. Preparing to unpack .../069-libpython3.11-dev_3.11.2-6_amd64.deb ... Unpacking libpython3.11-dev:amd64 (3.11.2-6) ... Selecting previously unselected package libpython3-dev:amd64. Preparing to unpack .../070-libpython3-dev_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-dev:amd64 (3.11.2-1+b1) ... Selecting previously unselected package libpython3-all-dev:amd64. Preparing to unpack .../071-libpython3-all-dev_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-all-dev:amd64 (3.11.2-1+b1) ... Selecting previously unselected package python-babel-localedata. Preparing to unpack .../072-python-babel-localedata_2.10.3-1_all.deb ... Unpacking python-babel-localedata (2.10.3-1) ... Selecting previously unselected package python3-alabaster. Preparing to unpack .../073-python3-alabaster_0.7.12-1_all.deb ... Unpacking python3-alabaster (0.7.12-1) ... Selecting previously unselected package python3-all. Preparing to unpack .../074-python3-all_3.11.2-1+b1_amd64.deb ... Unpacking python3-all (3.11.2-1+b1) ... Selecting previously unselected package python3.11-dev. Preparing to unpack .../075-python3.11-dev_3.11.2-6_amd64.deb ... Unpacking python3.11-dev (3.11.2-6) ... Selecting previously unselected package python3-dev. Preparing to unpack .../076-python3-dev_3.11.2-1+b1_amd64.deb ... Unpacking python3-dev (3.11.2-1+b1) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../077-python3-all-dev_3.11.2-1+b1_amd64.deb ... Unpacking python3-all-dev (3.11.2-1+b1) ... Selecting previously unselected package python3-attr. Preparing to unpack .../078-python3-attr_22.2.0-1_all.deb ... Unpacking python3-attr (22.2.0-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../079-python3-pkg-resources_66.1.1-1_all.deb ... Unpacking python3-pkg-resources (66.1.1-1) ... Selecting previously unselected package python3-tz. Preparing to unpack .../080-python3-tz_2022.7.1-4_all.deb ... Unpacking python3-tz (2022.7.1-4) ... Selecting previously unselected package python3-babel. Preparing to unpack .../081-python3-babel_2.10.3-1_all.deb ... Unpacking python3-babel (2.10.3-1) ... Selecting previously unselected package python3-certifi. Preparing to unpack .../082-python3-certifi_2022.9.24-1_all.deb ... Unpacking python3-certifi (2022.9.24-1) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../083-python3-chardet_5.1.0+dfsg-2_all.deb ... Unpacking python3-chardet (5.1.0+dfsg-2) ... Selecting previously unselected package python3-charset-normalizer. Preparing to unpack .../084-python3-charset-normalizer_3.0.1-2_all.deb ... Unpacking python3-charset-normalizer (3.0.1-2) ... Selecting previously unselected package python3-roman. Preparing to unpack .../085-python3-roman_3.3-3_all.deb ... Unpacking python3-roman (3.3-3) ... Selecting previously unselected package python3-docutils. Preparing to unpack .../086-python3-docutils_0.19+dfsg-6_all.deb ... Unpacking python3-docutils (0.19+dfsg-6) ... Selecting previously unselected package sphinx-common. Preparing to unpack .../087-sphinx-common_5.3.0-4_all.deb ... Unpacking sphinx-common (5.3.0-4) ... Selecting previously unselected package python3-imagesize. Preparing to unpack .../088-python3-imagesize_1.4.1-1_all.deb ... Unpacking python3-imagesize (1.4.1-1) ... Selecting previously unselected package python3-markupsafe. Preparing to unpack .../089-python3-markupsafe_2.1.2-1+b1_amd64.deb ... Unpacking python3-markupsafe (2.1.2-1+b1) ... Selecting previously unselected package python3-jinja2. Preparing to unpack .../090-python3-jinja2_3.1.2-1_all.deb ... Unpacking python3-jinja2 (3.1.2-1) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../091-python3-packaging_23.0-1_all.deb ... Unpacking python3-packaging (23.0-1) ... Selecting previously unselected package python3-pygments. Preparing to unpack .../092-python3-pygments_2.14.0+dfsg-1_all.deb ... Unpacking python3-pygments (2.14.0+dfsg-1) ... Selecting previously unselected package python3-idna. Preparing to unpack .../093-python3-idna_3.3-1_all.deb ... Unpacking python3-idna (3.3-1) ... Selecting previously unselected package python3-six. Preparing to unpack .../094-python3-six_1.16.0-4_all.deb ... Unpacking python3-six (1.16.0-4) ... Selecting previously unselected package python3-urllib3. Preparing to unpack .../095-python3-urllib3_1.26.12-1_all.deb ... Unpacking python3-urllib3 (1.26.12-1) ... Selecting previously unselected package python3-requests. Preparing to unpack .../096-python3-requests_2.28.1+dfsg-1_all.deb ... Unpacking python3-requests (2.28.1+dfsg-1) ... Selecting previously unselected package python3-snowballstemmer. Preparing to unpack .../097-python3-snowballstemmer_2.2.0-2_all.deb ... Unpacking python3-snowballstemmer (2.2.0-2) ... Selecting previously unselected package python3-sphinx. Preparing to unpack .../098-python3-sphinx_5.3.0-4_all.deb ... Unpacking python3-sphinx (5.3.0-4) ... Selecting previously unselected package python3-guzzle-sphinx-theme. Preparing to unpack .../099-python3-guzzle-sphinx-theme_0.7.11-6_all.deb ... Unpacking python3-guzzle-sphinx-theme (0.7.11-6) ... Selecting previously unselected package python3-iniconfig. Preparing to unpack .../100-python3-iniconfig_1.1.1-2_all.deb ... Unpacking python3-iniconfig (1.1.1-2) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../101-python3-more-itertools_8.10.0-2_all.deb ... Unpacking python3-more-itertools (8.10.0-2) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../102-python3-pluggy_1.0.0+repack-1_all.deb ... Unpacking python3-pluggy (1.0.0+repack-1) ... Selecting previously unselected package python3-py. Preparing to unpack .../103-python3-py_1.11.0-1_all.deb ... Unpacking python3-py (1.11.0-1) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../104-python3-pytest_7.2.1-2_all.deb ... Unpacking python3-pytest (7.2.1-2) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../105-python3-setuptools_66.1.1-1_all.deb ... Unpacking python3-setuptools (66.1.1-1) ... Selecting previously unselected package python3-pytest-runner. Preparing to unpack .../106-python3-pytest-runner_2.11.1-4_all.deb ... Unpacking python3-pytest-runner (2.11.1-4) ... Selecting previously unselected package python3-screed. Preparing to unpack .../107-python3-screed_1.0.5-4_all.deb ... Unpacking python3-screed (1.0.5-4) ... Selecting previously unselected package python3-sphinxcontrib.autoprogram. Preparing to unpack .../108-python3-sphinxcontrib.autoprogram_0.1.7-4_all.deb ... Unpacking python3-sphinxcontrib.autoprogram (0.1.7-4) ... Selecting previously unselected package rdfind. Preparing to unpack .../109-rdfind_1.5.0-1.1+b1_amd64.deb ... Unpacking rdfind (1.5.0-1.1+b1) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1) ... Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Setting up libdebhelper-perl (13.11.4) ... Setting up rdfind (1.5.0-1.1+b1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up python-babel-localedata (2.10.3-1) ... Setting up autotools-dev (20220109.1) ... Setting up libexpat1-dev:amd64 (2.5.0-1) ... Setting up libncurses6:amd64 (6.4-4) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up autopoint (0.21-12) ... Setting up autoconf (2.71-3) ... Setting up ruby-webrick (1.8.1-1) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libjson-perl (4.10000-1) ... Setting up fonts-liberation (1:1.07.4-11) ... Setting up libsub-override-perl (0.09-4) ... Setting up sgml-base (1.31) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up openssl (3.0.9-1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libbz2-dev:amd64 (1.0.8-5+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up xml-core (0.18+nmu1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up sphinx-common (5.3.0-4) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libpython3.11:amd64 (3.11.2-6) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up dh-exec (0.27) ... Setting up python3-markupsafe (2.1.2-1+b1) ... Setting up python3-tz (2022.7.1-4) ... Setting up python3-six (1.16.0-4) ... Setting up python3-roman (3.3-3) ... Setting up python3-jinja2 (3.1.2-1) ... Setting up python3-packaging (23.0-1) ... Setting up python3-certifi (2022.9.24-1) ... Setting up python3-snowballstemmer (2.2.0-2) ... Setting up libpython3.11-dev:amd64 (3.11.2-6) ... Setting up python3-idna (3.3-1) ... Setting up cython3 (0.29.32-2+b1) ... Setting up python3-urllib3 (1.26.12-1) ... Setting up python3-pluggy (1.0.0+repack-1) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up dh-python (5.20230130) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (22.2.0-1) ... Setting up libpython3-dev:amd64 (3.11.2-1+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-screed (1.0.5-4) ... Setting up python3-py (1.11.0-1) ... Setting up python3-babel (2.10.3-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3.11-dev (3.11.2-6) ... Setting up python3-charset-normalizer (3.0.1-2) ... Setting up python3-pytest (7.2.1-2) ... Setting up python3-alabaster (0.7.12-1) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-pygments (2.14.0+dfsg-1) ... Setting up python3-chardet (5.1.0+dfsg-2) ... Setting up libpython3-all-dev:amd64 (3.11.2-1+b1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up python3-requests (2.28.1+dfsg-1) ... Setting up python3-pytest-runner (2.11.1-4) ... Setting up python3-all-dev (3.11.2-1+b1) ... Setting up rake (13.0.6-3) ... Setting up ruby3.1 (3.1.2-7) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b1) ... Setting up libruby3.1:amd64 (3.1.2-7) ... Setting up libruby:amd64 (1:3.1) ... Setting up ruby (1:3.1) ... Setting up ruby-asciidoctor (2.0.18-2) ... Setting up asciidoctor (2.0.18-2) ... Setting up ruby-rubygems (3.3.15-2) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.19+dfsg-6) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.19+dfsg-6) ... Setting up python3-sphinx (5.3.0-4) ... Setting up python3-guzzle-sphinx-theme (0.7.11-6) ... Setting up python3-sphinxcontrib.autoprogram (0.1.7-4) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/3152983/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/3152983/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/khmer-3.0.0~a3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../khmer_3.0.0~a3+dfsg-4_source.changes dpkg-buildpackage: info: source package khmer dpkg-buildpackage: info: source version 3.0.0~a3+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra 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 '/build/khmer-3.0.0~a3+dfsg' dh_auto_clean || /bin/true pybuild --clean -i python{version} -p 3.11 I: pybuild base:240: python3.11 setup.py clean *** NOTE: Found Cython, extension files will be transpiled if this is an install invocation. /usr/lib/python3/dist-packages/setuptools/dist.py:775: 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 '/build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.11' 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 '/build/khmer-3.0.0~a3+dfsg/src/oxli' (cd ../../third-party/cqf && make clean) make[3]: Entering directory '/build/khmer-3.0.0~a3+dfsg/third-party/cqf' rm -f *.o gqf.o make[3]: Leaving directory '/build/khmer-3.0.0~a3+dfsg/third-party/cqf' rm -f *.o *.a *.so* oxli.pc make[2]: Leaving directory '/build/khmer-3.0.0~a3+dfsg/src/oxli' rm -rf __pycache__ .eggs make[1]: Leaving directory '/build/khmer-3.0.0~a3+dfsg' 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 ./khmer/_oxli/assembly.cpp ./khmer/_oxli/graphs.cpp ./khmer/_oxli/hashing.cpp ./khmer/_oxli/hashset.cpp ./khmer/_oxli/hllcounter.cpp ./khmer/_oxli/labeling.cpp ./khmer/_oxli/legacy_partitioning.cpp ./khmer/_oxli/parsing.cpp ./khmer/_oxli/readaligner.cpp ./khmer/_oxli/traversal.cpp ./khmer/_oxli/utils.cpp 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 pybuild --configure -i python{version} -p 3.11 I: pybuild base:240: python3.11 setup.py config *** NOTE: Found Cython, extension files will be transpiled if this is an install invocation. /usr/lib/python3/dist-packages/setuptools/dist.py:775: 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 '/build/khmer-3.0.0~a3+dfsg' dh_auto_build pybuild --build -i python{version} -p 3.11 I: pybuild base:240: /usr/bin/python3 setup.py build *** NOTE: Found Cython, extension files will be transpiled if this is an install invocation. /usr/lib/python3/dist-packages/setuptools/dist.py:775: 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 /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer copying khmer/kfile.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer copying khmer/khmer_args.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer copying khmer/utils.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer copying khmer/trimming.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer copying khmer/thread_utils.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer copying khmer/khmer_logger.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer copying khmer/_version.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer copying khmer/__init__.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer creating /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/khmer_tst_utils.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_read_parsers.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_version.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_threaded_sequence_processor.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_tabletype.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_subset_graph.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_streaming_io.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_sequence_validation.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_scripts.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_script_output.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_script_arguments.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_sandbox_scripts.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_read_handling.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_read_aligner.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_qfstorage.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_oxli_functions.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_normalize_by_median.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_nodegraph.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_nibblestorage.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_memory.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_lump.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_labelhash.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_hll.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_hashset.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_graph.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_functions.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_filter_abund.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_cython_parsing.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_cpython_hierarchy.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_counttable.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_counting_single.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_countgraph.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_banding.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_assembly.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/table_fixtures.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/graph_features.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/__init__.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests creating /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli copying oxli/partition.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli copying oxli/functions.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli copying oxli/build_graph.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli copying oxli/__init__.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli creating /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/__init__.py -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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 '*.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 'manual*' 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 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests creating /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.bz2 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.gz -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.truncated.bz2 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.truncated.gz -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/README.rst -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/all-A.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k12.ct -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k12.ht -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k32.stoptags -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k32.tagset -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/banding-reads.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/biglump-random-20-a.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/bogus.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/branched-genome.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/casava_18-pe.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/combine_parts_1.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-all-paired-all-keep.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-none-paired.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-some-paired-all-keep.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file.bz2 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file.gz -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/fakelump.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/fakelump.fa.stoptags.txt -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/filter-test-A.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/filter-test-B.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k12.ht -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k12.ht.gz -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k32.stoptags -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k32.tagset -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/multi-output.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/normC20k20.ct -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/old-style-format-w-comments.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.1 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.2 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.badleft -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.badright -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.paired_bad -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken2.fq.1 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken2.fq.2 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken3.fq.1 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken3.fq.2 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken4.fq.1 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken4.fq.2 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-2.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-broken.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-witherror.fa.pe -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa.pe -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa.se -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq.pe -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq.se -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq.1 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq.2 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa.1 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa.2 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq.1 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq.2 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired.malformat.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired.malformat.fq.2 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired_one.base.dif.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-X2.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.even.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.bz2 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.gz -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.part -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq.bz2 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq.gz -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.odd.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-b.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/random-31-c.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/readaligner-default.json -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/readaligner-k12.json -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/real-partition-small.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/real-partition-tiny.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/seq-a.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/seq-b.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/simple-genome-reads.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/simple-genome.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/single-read.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/single-read.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa.bz2 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa.gz -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.paired.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.paired2.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-3.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-impaired.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-paired.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-paired.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-empty.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-empty.fa.bz2 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-error-reads.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-n-reads.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-reads.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-reads.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-filter-abund-Ns.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph2.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph5.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-labels.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-large.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-multi.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-output-partitions.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-overlap1.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-overlap2.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fq.bz2 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fq.gz -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-short.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-contigs.fp -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-reads.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-reads.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-transcript.fa -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/truncated.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/unclean-reads.fastq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/valid-read-testing.fq -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying khmer/_oxli/assembly.pxd -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/assembly.pyx -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.pxd -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.pyx -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.pxd -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.pyx -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/hashset.pxd -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/hashset.pyx -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/hllcounter.pxd -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/hllcounter.pyx -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/labeling.pxd -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/labeling.pyx -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/legacy_partitioning.pxd -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/legacy_partitioning.pyx -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/oxli_exception_convert.cc -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/oxli_exception_convert.hh -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/oxli_types.pxd -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.pxd -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.pyx -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/readaligner.pxd -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/readaligner.pyx -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/traversal.pxd -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/traversal.pyx -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/utils.pxd -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/utils.pyx -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli UPDATING /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_version.py set /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_version.py to '3.0.0a3' running build_ext bash -c "cd third-party/cqf && make" make[2]: Entering directory '/build/khmer-3.0.0~a3+dfsg/third-party/cqf' g++ -std=c++11 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Ofast -I. -Wno-unused-result -Wno-strict-aliasing -Wno-unused-function gqf.c -c -o gqf.o make[2]: Leaving directory '/build/khmer-3.0.0~a3+dfsg/third-party/cqf' cythoning khmer/_oxli/utils.pyx to khmer/_oxli/utils.cpp cythoning khmer/_oxli/traversal.pyx to khmer/_oxli/traversal.cpp warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. cythoning khmer/_oxli/readaligner.pyx to khmer/_oxli/readaligner.cpp warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. cythoning khmer/_oxli/parsing.pyx to khmer/_oxli/parsing.cpp warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. cythoning khmer/_oxli/legacy_partitioning.pyx to khmer/_oxli/legacy_partitioning.cpp warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. cythoning khmer/_oxli/labeling.pyx to khmer/_oxli/labeling.cpp warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. cythoning khmer/_oxli/hllcounter.pyx to khmer/_oxli/hllcounter.cpp warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. cythoning khmer/_oxli/hashset.pyx to khmer/_oxli/hashset.cpp cythoning khmer/_oxli/hashing.pyx to khmer/_oxli/hashing.cpp cythoning khmer/_oxli/graphs.pyx to khmer/_oxli/graphs.cpp warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. cythoning khmer/_oxli/assembly.pyx to khmer/_oxli/assembly.cpp warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. building 'khmer._khmer' extension creating build creating build/temp.linux-x86_64-cpython-311 creating build/temp.linux-x86_64-cpython-311/src creating build/temp.linux-x86_64-cpython-311/src/khmer creating build/temp.linux-x86_64-cpython-311/src/oxli creating build/temp.linux-x86_64-cpython-311/third-party creating build/temp.linux-x86_64-cpython-311/third-party/smhasher x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o -O3 -std=c++11 -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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o -O3 -std=c++11 -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::shared_ptr >]': src/oxli/hashtable.cc:626:1: required from here src/oxli/hashtable.cc:138:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 138 | } 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::shared_ptr >]': src/oxli/hashtable.cc:643:1: required from here src/oxli/hashtable.cc:208:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 208 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_with_mask(oxli::read_parsers::ReadParserPtr&, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:662:1: required from here src/oxli/hashtable.cc:168:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 168 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding_with_mask(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:685:1: required from here src/oxli/hashtable.cc:250:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 250 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o -O3 -std=c++11 -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::shared_ptr >]': src/oxli/hllcounter.cc:435:1: required from here src/oxli/hllcounter.cc:366:40: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 366 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o -O3 -std=c++11 -fopenmp In file included from src/oxli/read_aligner.cc:48: include/oxli/read_aligner.hh:114:15: warning: 'oxli::freq_default' defined but not used [-Wunused-variable] 114 | static double freq_default[] = { log2(0.955), | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o -O3 -std=c++11 -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:40: 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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/storage.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/subset.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o -O3 -std=c++11 -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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o -O3 -std=c++11 -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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_khmer.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.utils' extension creating build/temp.linux-x86_64-cpython-311/khmer creating build/temp.linux-x86_64-cpython-311/khmer/_oxli x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/utils.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/utils.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.traversal' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/traversal.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/traversal.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/traversal.cpp:791: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/traversal.cpp:668: note: this is the location of the previous definition 668 | #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/traversal.cpp:675: note: this is the location of the previous definition 675 | #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/traversal.cpp:672: note: this is the location of the previous definition 672 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.readaligner' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/readaligner.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/readaligner.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/readaligner.cpp:791: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/readaligner.cpp:668: note: this is the location of the previous definition 668 | #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/readaligner.cpp:675: note: this is the location of the previous definition 675 | #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/readaligner.cpp:672: note: this is the location of the previous definition 672 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/readaligner.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.parsing' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/parsing.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/parsing.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/parsing.cpp:785: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/parsing.cpp:668: note: this is the location of the previous definition 668 | #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/parsing.cpp:675: note: this is the location of the previous definition 675 | #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/parsing.cpp:672: note: this is the location of the previous definition 672 | #define PyInt_FromLong PyLong_FromLong | khmer/_oxli/parsing.cpp: In function 'bool __pyx_f_5khmer_5_oxli_7parsing_sanitize_sequence(std::string&, std::string&, bool)': khmer/_oxli/parsing.cpp:5922:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5922 | 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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/parsing.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/parsing.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.legacy_partitioning' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/legacy_partitioning.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/legacy_partitioning.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/legacy_partitioning.cpp:791: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/legacy_partitioning.cpp:668: note: this is the location of the previous definition 668 | #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/legacy_partitioning.cpp:675: note: this is the location of the previous definition 675 | #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/legacy_partitioning.cpp:672: note: this is the location of the previous definition 672 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/legacy_partitioning.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.labeling' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/labeling.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/labeling.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/labeling.cpp:791: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/labeling.cpp:668: note: this is the location of the previous definition 668 | #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/labeling.cpp:675: note: this is the location of the previous definition 675 | #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/labeling.cpp:672: note: this is the location of the previous definition 672 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/labeling.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hllcounter' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/hllcounter.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/hllcounter.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/hllcounter.cpp:789: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/hllcounter.cpp:668: note: this is the location of the previous definition 668 | #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/hllcounter.cpp:675: note: this is the location of the previous definition 675 | #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/hllcounter.cpp:672: note: this is the location of the previous definition 672 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hllcounter.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hashset' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/hashset.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/hashset.o -O3 -std=c++11 -fopenmp In file included from /usr/include/c++/12/set:60, from khmer/_oxli/hashset.cpp:775: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::find(const _Key&) [with _Key = long long unsigned int; _Val = long long unsigned int; _KeyOfValue = std::_Identity; _Compare = std::less; _Alloc = std::allocator]', inlined from 'std::set<_Key, _Compare, _Alloc>::iterator std::set<_Key, _Compare, _Alloc>::find(const key_type&) [with _Key = long long unsigned int; _Compare = std::less; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_set.h:795:25, inlined from 'int __pyx_pf_5khmer_5_oxli_7hashset_7HashSet_10__contains__(__pyx_obj_5khmer_5_oxli_7hashset_HashSet*, PyObject*)' at khmer/_oxli/hashset.cpp:2536:35, inlined from 'int __pyx_pw_5khmer_5_oxli_7hashset_7HashSet_11__contains__(PyObject*, PyObject*)' at khmer/_oxli/hashset.cpp:2407:68: /usr/include/c++/12/bits/stl_tree.h:2533:15: warning: '__pyx_v_h' may be used uninitialized [-Wmaybe-uninitialized] 2532 | return (__j == end() | ~~~~~~~~~~~~~ 2533 | || _M_impl._M_key_compare(__k, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2534 | _S_key(__j._M_node))) ? end() : __j; | ~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/hashset.cpp: In function 'int __pyx_pw_5khmer_5_oxli_7hashset_7HashSet_11__contains__(PyObject*, PyObject*)': khmer/_oxli/hashset.cpp:2415:22: note: '__pyx_v_h' was declared here 2415 | oxli::HashIntoType __pyx_v_h; | ^~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/hashset.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashset.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hashing' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/hashing.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/hashing.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/hashing.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashing.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.graphs' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/graphs.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/graphs.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:791: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/graphs.cpp:668: note: this is the location of the previous definition 668 | #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:675: note: this is the location of the previous definition 675 | #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:672: note: this is the location of the previous definition 672 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/graphs.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.assembly' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/assembly.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/assembly.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:791: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/assembly.cpp:668: note: this is the location of the previous definition 668 | #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:675: note: this is the location of the previous definition 675 | #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:672: note: this is the location of the previous definition 672 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/assembly.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so -fopenmp running build_scripts creating build/scripts-3.11 copying and adjusting scripts/trim-low-abund.py -> build/scripts-3.11 copying and adjusting scripts/extract-paired-reads.py -> build/scripts-3.11 copying and adjusting scripts/unique-kmers.py -> build/scripts-3.11 copying and adjusting scripts/split-paired-reads.py -> build/scripts-3.11 copying and adjusting scripts/sample-reads-randomly.py -> build/scripts-3.11 copying and adjusting scripts/readstats.py -> build/scripts-3.11 copying and adjusting scripts/partition-graph.py -> build/scripts-3.11 copying and adjusting scripts/normalize-by-median.py -> build/scripts-3.11 copying and adjusting scripts/merge-partitions.py -> build/scripts-3.11 copying and adjusting scripts/make-initial-stoptags.py -> build/scripts-3.11 copying and adjusting scripts/load-into-counting.py -> build/scripts-3.11 copying and adjusting scripts/load-graph.py -> build/scripts-3.11 copying and adjusting scripts/interleave-reads.py -> build/scripts-3.11 copying and adjusting scripts/find-knots.py -> build/scripts-3.11 copying and adjusting scripts/filter-stoptags.py -> build/scripts-3.11 copying and adjusting scripts/filter-abund.py -> build/scripts-3.11 copying and adjusting scripts/filter-abund-single.py -> build/scripts-3.11 copying and adjusting scripts/fastq-to-fasta.py -> build/scripts-3.11 copying and adjusting scripts/extract-partitions.py -> build/scripts-3.11 copying and adjusting scripts/extract-long-sequences.py -> build/scripts-3.11 copying and adjusting scripts/do-partition.py -> build/scripts-3.11 copying and adjusting scripts/count-median.py -> build/scripts-3.11 copying and adjusting scripts/annotate-partitions.py -> build/scripts-3.11 copying and adjusting scripts/abundance-dist.py -> build/scripts-3.11 copying and adjusting scripts/abundance-dist-single.py -> build/scripts-3.11 changing mode of build/scripts-3.11/trim-low-abund.py from 644 to 755 changing mode of build/scripts-3.11/extract-paired-reads.py from 644 to 755 changing mode of build/scripts-3.11/unique-kmers.py from 644 to 755 changing mode of build/scripts-3.11/split-paired-reads.py from 644 to 755 changing mode of build/scripts-3.11/sample-reads-randomly.py from 644 to 755 changing mode of build/scripts-3.11/readstats.py from 644 to 755 changing mode of build/scripts-3.11/partition-graph.py from 644 to 755 changing mode of build/scripts-3.11/normalize-by-median.py from 644 to 755 changing mode of build/scripts-3.11/merge-partitions.py from 644 to 755 changing mode of build/scripts-3.11/make-initial-stoptags.py from 644 to 755 changing mode of build/scripts-3.11/load-into-counting.py from 644 to 755 changing mode of build/scripts-3.11/load-graph.py from 644 to 755 changing mode of build/scripts-3.11/interleave-reads.py from 644 to 755 changing mode of build/scripts-3.11/find-knots.py from 644 to 755 changing mode of build/scripts-3.11/filter-stoptags.py from 644 to 755 changing mode of build/scripts-3.11/filter-abund.py from 644 to 755 changing mode of build/scripts-3.11/filter-abund-single.py from 644 to 755 changing mode of build/scripts-3.11/fastq-to-fasta.py from 644 to 755 changing mode of build/scripts-3.11/extract-partitions.py from 644 to 755 changing mode of build/scripts-3.11/extract-long-sequences.py from 644 to 755 changing mode of build/scripts-3.11/do-partition.py from 644 to 755 changing mode of build/scripts-3.11/count-median.py from 644 to 755 changing mode of build/scripts-3.11/annotate-partitions.py from 644 to 755 changing mode of build/scripts-3.11/abundance-dist.py from 644 to 755 changing mode of build/scripts-3.11/abundance-dist-single.py from 644 to 755 ln -sf `pybuild --print build_dir|awk -F: '{print $2}'`/khmer/*.so khmer && \ ./setup.py develop --user && ./setup.py build_sphinx *** NOTE: Found Cython, extension files will be transpiled if this is an install invocation. /usr/lib/python3/dist-packages/setuptools/dist.py:775: 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:146: 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 '*.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 'manual*' 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 bash -c "cd third-party/cqf && make" make[2]: Entering directory '/build/khmer-3.0.0~a3+dfsg/third-party/cqf' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/khmer-3.0.0~a3+dfsg/third-party/cqf' skipping 'khmer/_oxli/utils.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/traversal.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/readaligner.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/parsing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/legacy_partitioning.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/labeling.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/hllcounter.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/hashset.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/hashing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/graphs.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/assembly.cpp' Cython extension (up-to-date) building 'khmer._khmer' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o -O3 -std=c++11 -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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o -O3 -std=c++11 -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::shared_ptr >]': src/oxli/hashtable.cc:626:1: required from here src/oxli/hashtable.cc:138:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 138 | } 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::shared_ptr >]': src/oxli/hashtable.cc:643:1: required from here src/oxli/hashtable.cc:208:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 208 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_with_mask(oxli::read_parsers::ReadParserPtr&, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:662:1: required from here src/oxli/hashtable.cc:168:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 168 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding_with_mask(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:685:1: required from here src/oxli/hashtable.cc:250:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 250 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o -O3 -std=c++11 -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::shared_ptr >]': src/oxli/hllcounter.cc:435:1: required from here src/oxli/hllcounter.cc:366:40: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 366 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o -O3 -std=c++11 -fopenmp In file included from src/oxli/read_aligner.cc:48: include/oxli/read_aligner.hh:114:15: warning: 'oxli::freq_default' defined but not used [-Wunused-variable] 114 | static double freq_default[] = { log2(0.955), | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o -O3 -std=c++11 -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:40: 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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/storage.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/subset.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o -O3 -std=c++11 -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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o -O3 -std=c++11 -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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -fopenmp creating build/lib.linux-x86_64-cpython-311 creating build/lib.linux-x86_64-cpython-311/khmer x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_khmer.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.utils' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/utils.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/utils.o -O3 -std=c++11 -fopenmp creating build/lib.linux-x86_64-cpython-311/khmer/_oxli x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.traversal' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/traversal.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/traversal.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/traversal.cpp:791: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/traversal.cpp:668: note: this is the location of the previous definition 668 | #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/traversal.cpp:675: note: this is the location of the previous definition 675 | #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/traversal.cpp:672: note: this is the location of the previous definition 672 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.readaligner' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/readaligner.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/readaligner.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/readaligner.cpp:791: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/readaligner.cpp:668: note: this is the location of the previous definition 668 | #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/readaligner.cpp:675: note: this is the location of the previous definition 675 | #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/readaligner.cpp:672: note: this is the location of the previous definition 672 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/readaligner.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.parsing' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/parsing.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/parsing.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/parsing.cpp:785: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/parsing.cpp:668: note: this is the location of the previous definition 668 | #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/parsing.cpp:675: note: this is the location of the previous definition 675 | #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/parsing.cpp:672: note: this is the location of the previous definition 672 | #define PyInt_FromLong PyLong_FromLong | khmer/_oxli/parsing.cpp: In function 'bool __pyx_f_5khmer_5_oxli_7parsing_sanitize_sequence(std::string&, std::string&, bool)': khmer/_oxli/parsing.cpp:5922:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5922 | 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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/parsing.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/parsing.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.legacy_partitioning' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/legacy_partitioning.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/legacy_partitioning.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/legacy_partitioning.cpp:791: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/legacy_partitioning.cpp:668: note: this is the location of the previous definition 668 | #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/legacy_partitioning.cpp:675: note: this is the location of the previous definition 675 | #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/legacy_partitioning.cpp:672: note: this is the location of the previous definition 672 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/legacy_partitioning.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.labeling' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/labeling.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/labeling.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/labeling.cpp:791: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/labeling.cpp:668: note: this is the location of the previous definition 668 | #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/labeling.cpp:675: note: this is the location of the previous definition 675 | #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/labeling.cpp:672: note: this is the location of the previous definition 672 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/labeling.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hllcounter' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/hllcounter.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/hllcounter.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/hllcounter.cpp:789: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/hllcounter.cpp:668: note: this is the location of the previous definition 668 | #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/hllcounter.cpp:675: note: this is the location of the previous definition 675 | #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/hllcounter.cpp:672: note: this is the location of the previous definition 672 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/hllcounter.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hashset' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/hashset.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/hashset.o -O3 -std=c++11 -fopenmp In file included from /usr/include/c++/12/set:60, from khmer/_oxli/hashset.cpp:775: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::find(const _Key&) [with _Key = long long unsigned int; _Val = long long unsigned int; _KeyOfValue = std::_Identity; _Compare = std::less; _Alloc = std::allocator]', inlined from 'std::set<_Key, _Compare, _Alloc>::iterator std::set<_Key, _Compare, _Alloc>::find(const key_type&) [with _Key = long long unsigned int; _Compare = std::less; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_set.h:795:25, inlined from 'int __pyx_pf_5khmer_5_oxli_7hashset_7HashSet_10__contains__(__pyx_obj_5khmer_5_oxli_7hashset_HashSet*, PyObject*)' at khmer/_oxli/hashset.cpp:2536:35, inlined from 'int __pyx_pw_5khmer_5_oxli_7hashset_7HashSet_11__contains__(PyObject*, PyObject*)' at khmer/_oxli/hashset.cpp:2407:68: /usr/include/c++/12/bits/stl_tree.h:2533:15: warning: '__pyx_v_h' may be used uninitialized [-Wmaybe-uninitialized] 2532 | return (__j == end() | ~~~~~~~~~~~~~ 2533 | || _M_impl._M_key_compare(__k, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2534 | _S_key(__j._M_node))) ? end() : __j; | ~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/hashset.cpp: In function 'int __pyx_pw_5khmer_5_oxli_7hashset_7HashSet_11__contains__(PyObject*, PyObject*)': khmer/_oxli/hashset.cpp:2415:22: note: '__pyx_v_h' was declared here 2415 | oxli::HashIntoType __pyx_v_h; | ^~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/hashset.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/hashset.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hashing' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/hashing.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/hashing.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/hashing.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/hashing.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.graphs' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/graphs.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/graphs.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:791: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/graphs.cpp:668: note: this is the location of the previous definition 668 | #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:675: note: this is the location of the previous definition 675 | #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:672: note: this is the location of the previous definition 672 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/graphs.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.assembly' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/assembly.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/assembly.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:791: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/assembly.cpp:668: note: this is the location of the previous definition 668 | #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:675: note: this is the location of the previous definition 675 | #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:672: note: this is the location of the previous definition 672 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/assembly.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so -fopenmp copying build/lib.linux-x86_64-cpython-311/khmer/_khmer.cpython-311-x86_64-linux-gnu.so -> khmer copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/parsing.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/hllcounter.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/hashset.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/hashing.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli Creating /build/khmer-3.0.0~a3+dfsg/fakehome/.local/lib/python3.11/site-packages/khmer.egg-link (link to .) Adding khmer 3.0.0a3 to easy-install.pth file Installing trim-low-abund.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing extract-paired-reads.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing unique-kmers.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing split-paired-reads.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing sample-reads-randomly.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing readstats.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing partition-graph.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing normalize-by-median.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing merge-partitions.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing make-initial-stoptags.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing load-into-counting.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing load-graph.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing interleave-reads.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing find-knots.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing filter-stoptags.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing filter-abund.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing filter-abund-single.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing fastq-to-fasta.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing extract-partitions.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing extract-long-sequences.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing do-partition.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing count-median.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing annotate-partitions.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing abundance-dist.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing abundance-dist-single.py script to /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installed /build/khmer-3.0.0~a3+dfsg Processing dependencies for khmer==3.0.0a3 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 /build/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Using /usr/lib/python3/dist-packages Finished processing dependencies for khmer==3.0.0a3 *** NOTE: Found Cython, extension files will be transpiled if this is an install invocation. /usr/lib/python3/dist-packages/setuptools/dist.py:775: 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 v5.3.0 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... /build/khmer-3.0.0~a3+dfsg/doc/dev/hackathon.rst: WARNING: document isn't included in any toctree /build/khmer-3.0.0~a3+dfsg/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 /build/khmer-3.0.0~a3+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: 'load-into-counting.py -N' /build/khmer-3.0.0~a3+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: 'load-into-counting.py --n_tables' /build/khmer-3.0.0~a3+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: 'load-into-counting.py -x' /build/khmer-3.0.0~a3+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: 'load-into-counting.py --max-tablesize' /build/khmer-3.0.0~a3+dfsg/doc/user/scripts.rst:79: WARNING: unknown option: '-x' /build/khmer-3.0.0~a3+dfsg/doc/user/scripts.rst:79: WARNING: unknown option: '-N' /build/khmer-3.0.0~a3+dfsg/doc/user/scripts.rst:87: WARNING: unknown option: '-x' /build/khmer-3.0.0~a3+dfsg/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 /usr/bin/make -C src/oxli clean make[2]: Entering directory '/build/khmer-3.0.0~a3+dfsg/src/oxli' (cd ../../third-party/cqf && make clean) make[3]: Entering directory '/build/khmer-3.0.0~a3+dfsg/third-party/cqf' rm -f *.o gqf.o make[3]: Leaving directory '/build/khmer-3.0.0~a3+dfsg/third-party/cqf' rm -f *.o *.a *.so* oxli.pc make[2]: Leaving directory '/build/khmer-3.0.0~a3+dfsg/src/oxli' /usr/bin/make -C src/oxli all USE_SYSTEM_ZLIB="true" USE_SYSTEM_LIBBZ2="true" make[2]: Entering directory '/build/khmer-3.0.0~a3+dfsg/src/oxli' (cd ../../third-party/cqf && make) make[3]: Entering directory '/build/khmer-3.0.0~a3+dfsg/third-party/cqf' g++ -std=c++11 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wshadow -Wcast-align -Wstrict-prototypes -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -fopenmp -DNO_UNIQUE_RC=0 -Wall -Ofast -I. -Wno-unused-result -Wno-strict-aliasing -Wno-unused-function gqf.c -c -o gqf.o cc1plus: warning: command-line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ gqf.c: In function 'void remove_replace_slots_and_shift_remainders_and_runends_and_offsets(QF*, int, uint64_t, uint64_t, const uint64_t*, uint64_t, uint64_t)': gqf.c:789:34: warning: declaration of 'i' shadows a previous local [-Wshadow] 789 | uint64_t i; | ^ gqf.c:748:18: note: shadowed declaration is here 748 | uint64_t i; | ^ gqf.c:834:42: warning: declaration of 'i' shadows a previous local [-Wshadow] 834 | uint64_t i; | ^ gqf.c:748:18: note: shadowed declaration is here 748 | uint64_t i; | ^ make[3]: Leaving directory '/build/khmer-3.0.0~a3+dfsg/third-party/cqf' g++ -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -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::shared_ptr >]': hashtable.cc:626:1: required from here hashtable.cc:138:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 138 | } 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::shared_ptr >]': hashtable.cc:643:1: required from here hashtable.cc:208:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 208 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_with_mask(oxli::read_parsers::ReadParserPtr&, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': hashtable.cc:662:1: required from here hashtable.cc:168:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 168 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding_with_mask(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': hashtable.cc:685:1: required from here hashtable.cc:250:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 250 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from hashtable.cc:49: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o hashgraph.o hashgraph.cc In file included from /usr/include/c++/12/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from ../../include/oxli/hashgraph.hh:52, from hashgraph.cc:47: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -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::shared_ptr >]': hllcounter.cc:435:1: required from here hllcounter.cc:366:40: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 366 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from hllcounter.cc:48: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o kmer_hash.o kmer_hash.cc In file included from /usr/include/c++/12/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from kmer_hash.cc:49: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o labelhash.o labelhash.cc In file included from /usr/include/c++/12/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from ../../include/oxli/hashgraph.hh:52, from labelhash.cc:44: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -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, | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from traversal.cc:38: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o read_aligner.o read_aligner.cc In file included from /usr/include/c++/12/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from read_aligner.cc:46: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from read_aligner.cc:48: ../../include/oxli/read_aligner.hh:114:15: warning: 'oxli::freq_default' defined but not used [-Wunused-variable] 114 | static double freq_default[] = { log2(0.955), | ^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -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:40: ../../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=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -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(); | ^~~~~ In file included from /usr/include/c++/12/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from ../../include/oxli/hashgraph.hh:52, from subset.cc:47: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o kmer_filters.o kmer_filters.cc In file included from /usr/include/c++/12/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from kmer_filters.cc:40: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -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) : | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/assembler.hh:43: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o alphabets.o alphabets.cc g++ -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -c -o murmur3.o ../../third-party/smhasher/MurmurHash3.cc g++ -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o storage.o storage.cc In file included from /usr/include/c++/12/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from storage.cc:44: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -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 ../../third-party/cqf/gqf.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 ../../third-party/cqf/gqf.o ranlib liboxli.a sed -e 's,@prefix@,/usr/local,' -e 's,@VERSION@,,' oxli.pc.in >oxli.pc make[2]: Leaving directory '/build/khmer-3.0.0~a3+dfsg/src/oxli' make[1]: Leaving directory '/build/khmer-3.0.0~a3+dfsg' 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 '/build/khmer-3.0.0~a3+dfsg' dh_auto_install install -m0755 -d /build/khmer-3.0.0\~a3\+dfsg/debian/tmp pybuild --install -i python{version} -p 3.11 --dest-dir /build/khmer-3.0.0\~a3\+dfsg/debian/tmp I: pybuild base:240: /usr/bin/python3 setup.py install --root '/build/khmer-3.0.0~a3+dfsg/debian/khmer' '--install-scripts=/usr/lib/khmer/bin' *** NOTE: Found Cython, extension files will be transpiled if this is an install invocation. /usr/lib/python3/dist-packages/setuptools/dist.py:775: 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 '*.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 'manual*' 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 -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.cpp -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.cpp -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/hashset.cpp -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/hllcounter.cpp -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/labeling.cpp -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/legacy_partitioning.cpp -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.cpp -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/readaligner.cpp -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/traversal.cpp -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/utils.cpp -> /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli UPDATING /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_version.py set /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_version.py to '3.0.0a3' running build_ext bash -c "cd third-party/cqf && make" make[2]: Entering directory '/build/khmer-3.0.0~a3+dfsg/third-party/cqf' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/khmer-3.0.0~a3+dfsg/third-party/cqf' skipping 'khmer/_oxli/utils.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/traversal.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/readaligner.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/parsing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/legacy_partitioning.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/labeling.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/hllcounter.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/hashset.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/hashing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/graphs.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/assembly.cpp' Cython extension (up-to-date) building 'khmer._khmer' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o -O3 -std=c++11 -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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o -O3 -std=c++11 -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::shared_ptr >]': src/oxli/hashtable.cc:626:1: required from here src/oxli/hashtable.cc:138:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 138 | } 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::shared_ptr >]': src/oxli/hashtable.cc:643:1: required from here src/oxli/hashtable.cc:208:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 208 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_with_mask(oxli::read_parsers::ReadParserPtr&, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:662:1: required from here src/oxli/hashtable.cc:168:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 168 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding_with_mask(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:685:1: required from here src/oxli/hashtable.cc:250:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 250 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o -O3 -std=c++11 -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::shared_ptr >]': src/oxli/hllcounter.cc:435:1: required from here src/oxli/hllcounter.cc:366:40: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 366 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o -O3 -std=c++11 -fopenmp In file included from src/oxli/read_aligner.cc:48: include/oxli/read_aligner.hh:114:15: warning: 'oxli::freq_default' defined but not used [-Wunused-variable] 114 | static double freq_default[] = { log2(0.955), | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o -O3 -std=c++11 -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:40: 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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/storage.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/subset.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o -O3 -std=c++11 -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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o -O3 -std=c++11 -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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_khmer.cpython-311-x86_64-linux-gnu.so -fopenmp running build_scripts running install_lib creating /build/khmer-3.0.0~a3+dfsg/debian/khmer creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11 creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/__init__.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/build_graph.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/functions.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/partition.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_khmer.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_version.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/utils.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/traversal.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/readaligner.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/parsing.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/legacy_partitioning.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/labeling.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hllcounter.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashset.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashing.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/graphs.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/assembly.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashing.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashset.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hllcounter.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/parsing.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/utils.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/utils.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/traversal.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/traversal.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/readaligner.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/readaligner.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/parsing.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/parsing.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/oxli_types.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/oxli_exception_convert.hh -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/oxli_exception_convert.cc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/legacy_partitioning.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/legacy_partitioning.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/labeling.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/labeling.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hllcounter.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hllcounter.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashset.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashset.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashing.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashing.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/graphs.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/graphs.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/assembly.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/assembly.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/__init__.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/valid-read-testing.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/unclean-reads.fastq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/truncated.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-transcript.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-sweep-reads.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-sweep-reads.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-sweep-contigs.fp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-short.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-reads.fq.gz -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-reads.fq.bz2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-reads.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-overlap2.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-overlap1.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-output-partitions.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-multi.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-large.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-labels.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-graph5.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-graph2.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-graph.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-filter-abund-Ns.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-fastq-reads.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-fastq-reads.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-fastq-n-reads.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-error-reads.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-empty.fa.bz2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-empty.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-paired.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-paired.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-impaired.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-3.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-2.paired2.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-2.paired.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-2.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.gz -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.bz2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-2.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/single-read.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/single-read.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/simple-genome.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/simple-genome-reads.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/seq-b.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/seq-a.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/real-partition-tiny.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/real-partition-small.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/readaligner-k12.json -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/readaligner-default.json -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-31-c.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-b.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.odd.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fq.gz -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fq.bz2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fa.part -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fa.gz -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fa.bz2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.even.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-X2.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired_one.base.dif.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.malformat.fq.2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.malformat.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fq.2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fq.1 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fa.2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fa.1 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-slash1.fq.2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-slash1.fq.1 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-slash1.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fq.se -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fq.pe -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fa.se -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fa.pe -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed-witherror.fa.pe -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed-broken.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed-2.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken4.fq.2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken4.fq.1 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken3.fq.2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken3.fq.1 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken2.fq.2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken2.fq.1 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken.fq.paired_bad -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken.fq.badright -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken.fq.badleft -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken.fq.2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken.fq.1 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/old-style-format-w-comments.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/normC20k20.ct -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/multi-output.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/goodversion-k32.tagset -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/goodversion-k32.stoptags -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/goodversion-k12.ht.gz -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/goodversion-k12.ht -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/filter-test-B.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/filter-test-A.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/fakelump.fa.stoptags.txt -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/fakelump.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/empty-file.gz -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/empty-file.bz2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/empty-file -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/dn-test-some-paired-all-keep.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/dn-test-none-paired.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/dn-test-all-paired-all-keep.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/combine_parts_1.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/casava_18-pe.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/branched-genome.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/bogus.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/biglump-random-20-a.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/banding-reads.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/badversion-k32.tagset -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/badversion-k32.stoptags -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/badversion-k12.ht -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/badversion-k12.ct -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/all-A.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/README.rst -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.gz -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.bz2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/100-reads.fq.gz -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/100-reads.fq.bz2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/.gitignore -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__init__.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/graph_features.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/table_fixtures.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_assembly.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_banding.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_countgraph.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_counting_single.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_counttable.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_cpython_hierarchy.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_cython_parsing.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_filter_abund.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_functions.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_graph.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_hashset.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_hll.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_labelhash.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_lump.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_memory.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_nibblestorage.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_nodegraph.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_normalize_by_median.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_oxli_functions.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_qfstorage.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_read_aligner.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_read_handling.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_sandbox_scripts.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_script_arguments.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_script_output.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_scripts.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_sequence_validation.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_streaming_io.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_subset_graph.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_tabletype.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_threaded_sequence_processor.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_version.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_read_parsers.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/khmer_tst_utils.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/__init__.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/khmer_logger.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/thread_utils.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/trimming.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/utils.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/khmer_args.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/kfile.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/__init__.py to __init__.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/build_graph.py to build_graph.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/functions.py to functions.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/partition.py to partition.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_version.py to _version.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli/__init__.py to __init__.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__init__.py to __init__.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/graph_features.py to graph_features.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/table_fixtures.py to table_fixtures.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_assembly.py to test_assembly.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_banding.py to test_banding.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_countgraph.py to test_countgraph.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_counting_single.py to test_counting_single.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_counttable.py to test_counttable.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_cpython_hierarchy.py to test_cpython_hierarchy.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_cython_parsing.py to test_cython_parsing.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_filter_abund.py to test_filter_abund.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_functions.py to test_functions.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_graph.py to test_graph.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_hashset.py to test_hashset.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_hll.py to test_hll.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_labelhash.py to test_labelhash.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_lump.py to test_lump.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_memory.py to test_memory.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_nibblestorage.py to test_nibblestorage.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_nodegraph.py to test_nodegraph.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_normalize_by_median.py to test_normalize_by_median.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_oxli_functions.py to test_oxli_functions.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_qfstorage.py to test_qfstorage.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_read_aligner.py to test_read_aligner.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_read_handling.py to test_read_handling.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_sandbox_scripts.py to test_sandbox_scripts.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_script_arguments.py to test_script_arguments.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_script_output.py to test_script_output.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_scripts.py to test_scripts.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_sequence_validation.py to test_sequence_validation.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_streaming_io.py to test_streaming_io.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py to test_subset_graph.cpython-311.pyc /usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py:61: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py:82: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py:278: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py:476: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py:509: SyntaxWarning: "is" with a literal. Did you mean "=="? byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_tabletype.py to test_tabletype.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_threaded_sequence_processor.py to test_threaded_sequence_processor.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_version.py to test_version.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_read_parsers.py to test_read_parsers.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/khmer_tst_utils.py to khmer_tst_utils.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__init__.py to __init__.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/khmer_logger.py to khmer_logger.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/thread_utils.py to thread_utils.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/trimming.py to trimming.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/utils.py to utils.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/khmer_args.py to khmer_args.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/kfile.py to kfile.cpython-311.pyc running install_egg_info Copying khmer.egg-info to /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer-3.0.0a3.egg-info Skipping SOURCES.txt running install_scripts creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/abundance-dist-single.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/abundance-dist.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/annotate-partitions.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/count-median.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/do-partition.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/extract-long-sequences.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/extract-partitions.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/fastq-to-fasta.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/filter-abund-single.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/filter-abund.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/filter-stoptags.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/find-knots.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/interleave-reads.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/load-graph.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/load-into-counting.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/make-initial-stoptags.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/merge-partitions.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/normalize-by-median.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/partition-graph.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/readstats.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/sample-reads-randomly.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/split-paired-reads.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/unique-kmers.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/extract-paired-reads.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/trim-low-abund.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/abundance-dist-single.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/abundance-dist.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/annotate-partitions.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/count-median.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/do-partition.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/extract-long-sequences.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/extract-partitions.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/fastq-to-fasta.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/filter-abund-single.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/filter-abund.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/filter-stoptags.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/find-knots.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/interleave-reads.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/load-graph.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/load-into-counting.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/make-initial-stoptags.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/merge-partitions.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/normalize-by-median.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/partition-graph.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/readstats.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/sample-reads-randomly.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/split-paired-reads.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/unique-kmers.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/extract-paired-reads.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/trim-low-abund.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 3.11 I: pybuild base:240: cd '/build/khmer-3.0.0~a3+dfsg'; export PATH='/build/khmer-3.0.0~a3+dfsg/debian/khmer'/usr/lib/khmer/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path ; cd '/build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build'; export PYTHONPATH=/build/khmer-3.0.0~a3+dfsg; python3.11 -m pytest -m 'not known_failing and not jenkins and not huge and not noroot' -q ============================= test session starts ============================== platform linux -- Python 3.11.2, pytest-7.2.1, pluggy-1.0.0+repack rootdir: /build/khmer-3.0.0~a3+dfsg, configfile: pytest.ini collected 2984 items / 94 deselected / 2890 selected khmer/tests/test_assembly.py ........................................... [ 1%] ........................................................................ [ 3%] ........................................................................ [ 6%] ........................................................................ [ 8%] ........................................................................ [ 11%] .......................... [ 12%] khmer/tests/test_banding.py ............ [ 12%] khmer/tests/test_countgraph.py ......................................... [ 14%] ................................................ [ 15%] khmer/tests/test_counting_single.py ......................... [ 16%] khmer/tests/test_counttable.py ..................... [ 17%] khmer/tests/test_cpython_hierarchy.py .... [ 17%] khmer/tests/test_cython_parsing.py ..................................... [ 18%] .... [ 18%] khmer/tests/test_filter_abund.py ................... [ 19%] khmer/tests/test_functions.py .................. [ 20%] khmer/tests/test_graph.py ............................ [ 21%] khmer/tests/test_hashset.py .............. [ 21%] khmer/tests/test_hll.py ......................... [ 22%] khmer/tests/test_labelhash.py ...................... [ 23%] khmer/tests/test_lump.py ...... [ 23%] khmer/tests/test_memory.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 .... [ 27%] khmer/tests/test_qfstorage.py . [ 27%] khmer/tests/test_read_aligner.py ................ [ 28%] khmer/tests/test_read_handling.py ................................ [ 29%] khmer/tests/test_read_parsers.py .............................. [ 30%] khmer/tests/test_sandbox_scripts.py ssssssssssssssssss [ 31%] khmer/tests/test_script_arguments.py ............................. [ 32%] khmer/tests/test_script_output.py ........... [ 32%] khmer/tests/test_scripts.py ............................................ [ 34%] ........................................................................ [ 36%] .............................. [ 37%] khmer/tests/test_sequence_validation.py ................................ [ 38%] ................... [ 39%] khmer/tests/test_streaming_io.py ............................ [ 40%] khmer/tests/test_subset_graph.py ........................... [ 41%] khmer/tests/test_tabletype.py .......................................... [ 42%] ........s.s.ss.......................................................... [ 45%] ........................................................................ [ 47%] ........................................................... [ 49%] khmer/tests/test_threaded_sequence_processor.py ...... [ 49%] khmer/tests/test_version.py . [ 50%] tests/test_assembly.py ................................................. [ 51%] ........................................................................ [ 54%] ........................................................................ [ 56%] ........................................................................ [ 59%] ........................................................................ [ 61%] .................... [ 62%] tests/test_banding.py ............ [ 62%] tests/test_countgraph.py ............................................... [ 64%] .......................................... [ 65%] tests/test_counting_single.py ......................... [ 66%] tests/test_counttable.py ..................... [ 67%] tests/test_cpython_hierarchy.py .... [ 67%] tests/test_cython_parsing.py ......................................... [ 68%] tests/test_filter_abund.py ................... [ 69%] tests/test_functions.py .................. [ 70%] tests/test_graph.py ............................ [ 71%] tests/test_hashset.py .............. [ 71%] tests/test_hll.py ......................... [ 72%] tests/test_labelhash.py ...................... [ 73%] tests/test_lump.py ...... [ 73%] tests/test_memory.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 .... [ 77%] tests/test_qfstorage.py . [ 77%] tests/test_read_aligner.py ................ [ 78%] tests/test_read_handling.py ................................ [ 79%] tests/test_read_parsers.py .............................. [ 80%] tests/test_sandbox_scripts.py ssssssssssssssssss [ 81%] tests/test_script_arguments.py ............................. [ 82%] tests/test_script_output.py ........... [ 82%] tests/test_scripts.py .................................................. [ 84%] ........................................................................ [ 86%] ........................ [ 87%] tests/test_sequence_validation.py ...................................... [ 88%] ............. [ 89%] tests/test_streaming_io.py ............................ [ 90%] tests/test_subset_graph.py ........................... [ 91%] tests/test_tabletype.py ................................................ [ 92%] ..s.s.ss................................................................ [ 95%] ........................................................................ [ 97%] ..................................................... [ 99%] tests/test_threaded_sequence_processor.py ...... [ 99%] tests/test_version.py . [100%] ========= 2846 passed, 44 skipped, 94 deselected in 345.02s (0:05:45) ========== rm -fr -- /tmp/dh-xdg-rundir-vn3sWstu make[1]: Leaving directory '/build/khmer-3.0.0~a3+dfsg' 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 -m0755 -d /build/khmer-3.0.0\~a3\+dfsg/debian/tmp pybuild --install -i python{version} -p 3.11 --dest-dir /build/khmer-3.0.0\~a3\+dfsg/debian/tmp I: pybuild base:240: /usr/bin/python3 setup.py install --root '/build/khmer-3.0.0~a3+dfsg/debian/khmer' '--install-scripts=/usr/lib/khmer/bin' *** NOTE: Found Cython, extension files will be transpiled if this is an install invocation. /usr/lib/python3/dist-packages/setuptools/dist.py:775: 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 '*.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 'manual*' 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 /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_version.py set /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_version.py to '3.0.0a3' running build_ext bash -c "cd third-party/cqf && make" make[1]: Entering directory '/build/khmer-3.0.0~a3+dfsg/third-party/cqf' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/build/khmer-3.0.0~a3+dfsg/third-party/cqf' skipping 'khmer/_oxli/utils.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/traversal.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/readaligner.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/parsing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/legacy_partitioning.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/labeling.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/hllcounter.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/hashset.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/hashing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/graphs.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/assembly.cpp' Cython extension (up-to-date) building 'khmer._khmer' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o -O3 -std=c++11 -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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o -O3 -std=c++11 -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::shared_ptr >]': src/oxli/hashtable.cc:626:1: required from here src/oxli/hashtable.cc:138:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 138 | } 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::shared_ptr >]': src/oxli/hashtable.cc:643:1: required from here src/oxli/hashtable.cc:208:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 208 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_with_mask(oxli::read_parsers::ReadParserPtr&, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:662:1: required from here src/oxli/hashtable.cc:168:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 168 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding_with_mask(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:685:1: required from here src/oxli/hashtable.cc:250:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 250 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o -O3 -std=c++11 -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::shared_ptr >]': src/oxli/hllcounter.cc:435:1: required from here src/oxli/hllcounter.cc:366:40: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 366 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o -O3 -std=c++11 -fopenmp In file included from src/oxli/read_aligner.cc:48: include/oxli/read_aligner.hh:114:15: warning: 'oxli::freq_default' defined but not used [-Wunused-variable] 114 | static double freq_default[] = { log2(0.955), | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o -O3 -std=c++11 -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:40: 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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/storage.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/subset.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o -O3 -std=c++11 -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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o -O3 -std=c++11 -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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_khmer.cpython-311-x86_64-linux-gnu.so -fopenmp running build_scripts running install_lib creating /build/khmer-3.0.0~a3+dfsg/debian/khmer creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11 creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/__pycache__/partition.cpython-311.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/__pycache__/functions.cpython-311.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/__pycache__/build_graph.cpython-311.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/__pycache__/__init__.cpython-311.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/__init__.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/build_graph.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/functions.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/partition.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_khmer.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_version.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/__pycache__/trimming.cpython-311.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/__pycache__/thread_utils.cpython-311.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/__pycache__/kfile.cpython-311.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/__pycache__/khmer_logger.cpython-311.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/__pycache__/utils.cpython-311.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/__pycache__/khmer_args.cpython-311.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/__pycache__/_version.cpython-311.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/__pycache__/__init__.cpython-311.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__pycache__ creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/__pycache__/__init__.cpython-311.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/utils.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/traversal.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/readaligner.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/parsing.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/legacy_partitioning.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/labeling.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hllcounter.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashset.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashing.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/graphs.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/assembly.cpp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashing.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashset.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hllcounter.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/parsing.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/utils.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/utils.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/traversal.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/traversal.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/readaligner.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/readaligner.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/parsing.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/parsing.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/oxli_types.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/oxli_exception_convert.hh -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/oxli_exception_convert.cc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/legacy_partitioning.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/legacy_partitioning.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/labeling.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/labeling.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hllcounter.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hllcounter.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashset.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashset.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashing.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashing.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/graphs.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/graphs.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/assembly.pyx -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/assembly.pxd -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/__init__.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_version.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_threaded_sequence_processor.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_tabletype.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_subset_graph.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_streaming_io.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/table_fixtures.cpython-311.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_sequence_validation.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_script_output.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_script_arguments.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_sandbox_scripts.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_read_parsers.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_read_handling.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_read_aligner.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_qfstorage.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_oxli_functions.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_normalize_by_median.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_nodegraph.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_nibblestorage.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_memory.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_lump.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_labelhash.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_hll.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_hashset.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_graph.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_functions.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_scripts.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_filter_abund.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_cython_parsing.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_cpython_hierarchy.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_counttable.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_counting_single.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_countgraph.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_banding.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/graph_features.cpython-311.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/khmer_tst_utils.cpython-311.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/test_assembly.cpython-311-pytest-7.2.1.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__pycache__/__init__.cpython-311.pyc -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__pycache__ creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/valid-read-testing.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/unclean-reads.fastq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/truncated.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-transcript.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-sweep-reads.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-sweep-reads.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-sweep-contigs.fp -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-short.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-reads.fq.gz -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-reads.fq.bz2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-reads.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-overlap2.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-overlap1.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-output-partitions.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-multi.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-large.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-labels.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-graph5.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-graph2.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-graph.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-filter-abund-Ns.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-fastq-reads.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-fastq-reads.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-fastq-n-reads.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-error-reads.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-empty.fa.bz2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-empty.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-paired.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-paired.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-impaired.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-3.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-2.paired2.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-2.paired.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-2.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.gz -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.bz2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-2.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/single-read.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/single-read.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/simple-genome.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/simple-genome-reads.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/seq-b.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/seq-a.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/real-partition-tiny.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/real-partition-small.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/readaligner-k12.json -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/readaligner-default.json -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-31-c.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-b.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.odd.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fq.gz -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fq.bz2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fa.part -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fa.gz -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fa.bz2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.even.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-X2.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired_one.base.dif.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.malformat.fq.2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.malformat.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fq.2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fq.1 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fa.2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fa.1 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-slash1.fq.2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-slash1.fq.1 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-slash1.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fq.se -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fq.pe -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fa.se -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fa.pe -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed-witherror.fa.pe -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed-broken.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed-2.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken4.fq.2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken4.fq.1 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken3.fq.2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken3.fq.1 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken2.fq.2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken2.fq.1 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken.fq.paired_bad -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken.fq.badright -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken.fq.badleft -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken.fq.2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken.fq.1 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/old-style-format-w-comments.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/normC20k20.ct -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/multi-output.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/goodversion-k32.tagset -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/goodversion-k32.stoptags -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/goodversion-k12.ht.gz -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/goodversion-k12.ht -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/filter-test-B.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/filter-test-A.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/fakelump.fa.stoptags.txt -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/fakelump.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/empty-file.gz -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/empty-file.bz2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/empty-file -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/dn-test-some-paired-all-keep.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/dn-test-none-paired.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/dn-test-all-paired-all-keep.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/combine_parts_1.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/casava_18-pe.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/branched-genome.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/bogus.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/biglump-random-20-a.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/banding-reads.fq -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/badversion-k32.tagset -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/badversion-k32.stoptags -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/badversion-k12.ht -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/badversion-k12.ct -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/all-A.fa -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/README.rst -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.gz -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.bz2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/100-reads.fq.gz -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/100-reads.fq.bz2 -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/.gitignore -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__init__.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/graph_features.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/table_fixtures.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_assembly.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_banding.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_countgraph.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_counting_single.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_counttable.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_cpython_hierarchy.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_cython_parsing.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_filter_abund.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_functions.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_graph.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_hashset.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_hll.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_labelhash.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_lump.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_memory.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_nibblestorage.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_nodegraph.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_normalize_by_median.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_oxli_functions.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_qfstorage.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_read_aligner.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_read_handling.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_sandbox_scripts.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_script_arguments.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_script_output.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_scripts.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_sequence_validation.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_streaming_io.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_subset_graph.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_tabletype.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_threaded_sequence_processor.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_version.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_read_parsers.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/khmer_tst_utils.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/__init__.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/khmer_logger.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/thread_utils.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/trimming.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/utils.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/khmer_args.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/kfile.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/__init__.py to __init__.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/build_graph.py to build_graph.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/functions.py to functions.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/partition.py to partition.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_version.py to _version.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli/__init__.py to __init__.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__init__.py to __init__.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/graph_features.py to graph_features.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/table_fixtures.py to table_fixtures.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_assembly.py to test_assembly.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_banding.py to test_banding.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_countgraph.py to test_countgraph.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_counting_single.py to test_counting_single.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_counttable.py to test_counttable.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_cpython_hierarchy.py to test_cpython_hierarchy.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_cython_parsing.py to test_cython_parsing.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_filter_abund.py to test_filter_abund.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_functions.py to test_functions.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_graph.py to test_graph.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_hashset.py to test_hashset.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_hll.py to test_hll.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_labelhash.py to test_labelhash.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_lump.py to test_lump.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_memory.py to test_memory.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_nibblestorage.py to test_nibblestorage.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_nodegraph.py to test_nodegraph.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_normalize_by_median.py to test_normalize_by_median.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_oxli_functions.py to test_oxli_functions.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_qfstorage.py to test_qfstorage.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_read_aligner.py to test_read_aligner.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_read_handling.py to test_read_handling.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_sandbox_scripts.py to test_sandbox_scripts.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_script_arguments.py to test_script_arguments.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_script_output.py to test_script_output.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_scripts.py to test_scripts.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_sequence_validation.py to test_sequence_validation.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_streaming_io.py to test_streaming_io.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py to test_subset_graph.cpython-311.pyc /usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py:61: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py:82: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py:278: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py:476: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py:509: SyntaxWarning: "is" with a literal. Did you mean "=="? byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_tabletype.py to test_tabletype.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_threaded_sequence_processor.py to test_threaded_sequence_processor.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_version.py to test_version.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_read_parsers.py to test_read_parsers.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/khmer_tst_utils.py to khmer_tst_utils.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__init__.py to __init__.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/khmer_logger.py to khmer_logger.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/thread_utils.py to thread_utils.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/trimming.py to trimming.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/utils.py to utils.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/khmer_args.py to khmer_args.cpython-311.pyc byte-compiling /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/kfile.py to kfile.cpython-311.pyc running install_egg_info Copying khmer.egg-info to /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer-3.0.0a3.egg-info Skipping SOURCES.txt running install_scripts creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer creating /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/abundance-dist-single.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/abundance-dist.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/annotate-partitions.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/count-median.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/do-partition.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/extract-long-sequences.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/extract-partitions.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/fastq-to-fasta.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/filter-abund-single.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/filter-abund.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/filter-stoptags.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/find-knots.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/interleave-reads.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/load-graph.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/load-into-counting.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/make-initial-stoptags.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/merge-partitions.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/normalize-by-median.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/partition-graph.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/readstats.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/sample-reads-randomly.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/split-paired-reads.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/unique-kmers.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/extract-paired-reads.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/trim-low-abund.py -> /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/abundance-dist-single.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/abundance-dist.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/annotate-partitions.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/count-median.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/do-partition.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/extract-long-sequences.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/extract-partitions.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/fastq-to-fasta.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/filter-abund-single.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/filter-abund.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/filter-stoptags.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/find-knots.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/interleave-reads.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/load-graph.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/load-into-counting.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/make-initial-stoptags.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/merge-partitions.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/normalize-by-median.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/partition-graph.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/readstats.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/sample-reads-randomly.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/split-paired-reads.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/unique-kmers.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/extract-paired-reads.py to 755 changing mode of /build/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/trim-low-abund.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 '/build/khmer-3.0.0~a3+dfsg' cd src/oxli && /usr/bin/make PREFIX=../debian/tmp install make[2]: Entering directory '/build/khmer-3.0.0~a3+dfsg/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 '/build/khmer-3.0.0~a3+dfsg/src/oxli' dh_install install -m0755 -d debian/khmer-common/usr/share/file/khmer cp --reflink=auto -a ./include/oxli/magic debian/khmer-common/usr/share/file/khmer/ install -m0755 -d debian/khmer//usr/share/metainfo/ cp --reflink=auto -a ./debian/khmer.metainfo.xml debian/khmer//usr/share/metainfo// install -m0755 -d debian/khmer/usr/bin/ cp --reflink=auto -a ./debian/bin/khmer debian/khmer/usr/bin// install -m0755 -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 -m0755 -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 -m0755 -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 -m0755 -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 -m0755 -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/ find debian/khmer -name .gitignore -delete make[1]: Leaving directory '/build/khmer-3.0.0~a3+dfsg' dh_installdocs -O--buildsystem=pybuild install -m0755 -d debian/khmer-common/usr/share/doc/khmer-common install -m0755 -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 {} /build/khmer-3.0.0~a3+dfsg/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 -m0755 -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 -m0755 -d debian/khmer/usr/share/doc/khmer install -p -m0644 debian/copyright debian/khmer/usr/share/doc/khmer/copyright install -m0755 -d debian/liboxli1/usr/share/doc/liboxli1 install -p -m0644 debian/copyright debian/liboxli1/usr/share/doc/liboxli1/copyright install -m0755 -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 '/build/khmer-3.0.0~a3+dfsg' dh_sphinxdoc ln -sf ../../../../javascript/sphinxdoc/1.0/doctools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js ln -sf ../../../../javascript/sphinxdoc/1.0/underscore.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js 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/searchtools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.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/jquery.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.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/language_data.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js ln -sf ../../../../javascript/sphinxdoc/1.0/_sphinx_javascript_frameworks_compat.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/_sphinx_javascript_frameworks_compat.js ln -sf ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.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/copyright debian/khmer-common/usr/share/doc/khmer-common/test-compile.cc debian/khmer-common/usr/share/doc/khmer-common/run-unit-test debian/khmer-common/usr/share/doc/khmer-common/README.test debian/khmer-common/usr/share/doc/khmer-common/README.rst debian/khmer-common/usr/share/doc/khmer-common/html debian/khmer-common/usr/share/doc/khmer-common/html/user debian/khmer-common/usr/share/doc/khmer-common/html/user/scripts.html debian/khmer-common/usr/share/doc/khmer-common/html/user/partitioning-big-data.html debian/khmer-common/usr/share/doc/khmer-common/html/user/known-issues.html debian/khmer-common/usr/share/doc/khmer-common/html/user/install.html debian/khmer-common/usr/share/doc/khmer-common/html/user/index.html debian/khmer-common/usr/share/doc/khmer-common/html/user/guide.html debian/khmer-common/usr/share/doc/khmer-common/html/user/getting-help.html debian/khmer-common/usr/share/doc/khmer-common/html/user/galaxy.html debian/khmer-common/usr/share/doc/khmer-common/html/user/examples.html debian/khmer-common/usr/share/doc/khmer-common/html/user/choosing-table-sizes.html debian/khmer-common/usr/share/doc/khmer-common/html/user/blog-posts.html debian/khmer-common/usr/share/doc/khmer-common/html/user/biblio.html debian/khmer-common/usr/share/doc/khmer-common/html/user/api-examples.html debian/khmer-common/usr/share/doc/khmer-common/html/searchindex.js debian/khmer-common/usr/share/doc/khmer-common/html/search.html debian/khmer-common/usr/share/doc/khmer-common/html/roadmap.html debian/khmer-common/usr/share/doc/khmer-common/html/release-notes debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-2.1.html debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-2.0.html debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.4.html debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.3.html debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.2.html debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.1.html debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.0.html debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.0.1.html debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/index.html debian/khmer-common/usr/share/doc/khmer-common/html/objects.inv debian/khmer-common/usr/share/doc/khmer-common/html/introduction.html debian/khmer-common/usr/share/doc/khmer-common/html/index.html debian/khmer-common/usr/share/doc/khmer-common/html/genindex.html debian/khmer-common/usr/share/doc/khmer-common/html/dev debian/khmer-common/usr/share/doc/khmer-common/html/dev/scripts-and-sandbox.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/release.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/python-api.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/index.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/hackathon.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/guidelines-continued-dev.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/getting-started.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/for-khmer-developers.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/development.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/codebase-guide.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/binary-file-formats.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/a-quick-guide-to-testing.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/CODE_OF_CONDUCT.html debian/khmer-common/usr/share/doc/khmer-common/html/contributors.html debian/khmer-common/usr/share/doc/khmer-common/html/_static debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/pygments.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/plus.png debian/khmer-common/usr/share/doc/khmer-common/html/_static/minus.png debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/labibi.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/labibi.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/jquery.min.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/guzzle.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/source-serif-pro.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/bower.json debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Semibold.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Regular.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Light.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-ExtraLight.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Bold.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Black.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Semibold.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Regular.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Light.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-ExtraLight.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Bold.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Black.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Semibold.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Regular.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Light.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-ExtraLight.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Bold.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Black.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/SourceSerifProReadMe.html debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/ReadMe.html debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/README.md debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Semibold.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Regular.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Light.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-ExtraLight.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Bold.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Black.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Semibold.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Regular.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Light.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-ExtraLight.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Bold.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Black.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/stylesheet.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts debian/khmer-common/usr/share/doc/khmer-common/html/_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.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_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.eot debian/khmer-common/usr/share/doc/khmer-common/html/_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.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_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.eot debian/khmer-common/usr/share/doc/khmer-common/html/_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.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_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.eot debian/khmer-common/usr/share/doc/khmer-common/html/_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.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_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.eot debian/khmer-common/usr/share/doc/khmer-common/html/_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.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_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.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_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.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_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.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_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.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_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.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.woff2 debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.woff 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.svg 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/LiberationSerif-Regular.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSans-Regular.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSans-Italic.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/file.png debian/khmer-common/usr/share/doc/khmer-common/html/_static/documentation_options.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/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/css/bootstrap-theme.min.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/basic.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/_sphinx_javascript_frameworks_compat.js debian/khmer-common/usr/share/doc/khmer-common/html/_sources debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/scripts.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/partitioning-big-data.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/known-issues.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/install.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/index.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/guide.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/getting-help.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/galaxy.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/examples.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/choosing-table-sizes.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/blog-posts.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/biblio.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/api-examples.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/roadmap.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes 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-2.0.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.4.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/release-notes/release-1.2.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.1.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-1.0.1.rst.txt 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/introduction.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/index.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/scripts-and-sandbox.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/release.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/python-api.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/index.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/hackathon.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/guidelines-continued-dev.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/getting-started.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/for-khmer-developers.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/development.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/codebase-guide.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/binary-file-formats.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/a-quick-guide-to-testing.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/CODE_OF_CONDUCT.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/contributors.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/LICENSE.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_images debian/khmer-common/usr/share/doc/khmer-common/html/_images/partitioning-workflow.png debian/khmer-common/usr/share/doc/khmer-common/html/_images/artifact-removal.png debian/khmer-common/usr/share/doc/khmer-common/html/LICENSE.html debian/khmer-common/usr/share/doc/khmer-common/html/.buildinfo 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/sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/_sphinx_javascript_frameworks_compat.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/_sphinx_javascript_frameworks_compat.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//_sphinx_javascript_frameworks_compat.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//_sphinx_javascript_frameworks_compat.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/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/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/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/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/sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/_sphinx_javascript_frameworks_compat.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/_sphinx_javascript_frameworks_compat.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//_sphinx_javascript_frameworks_compat.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//_sphinx_javascript_frameworks_compat.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/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/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/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/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/sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/_sphinx_javascript_frameworks_compat.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/_sphinx_javascript_frameworks_compat.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//_sphinx_javascript_frameworks_compat.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//_sphinx_javascript_frameworks_compat.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/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/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/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/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/sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/_sphinx_javascript_frameworks_compat.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/_sphinx_javascript_frameworks_compat.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//_sphinx_javascript_frameworks_compat.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//_sphinx_javascript_frameworks_compat.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/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/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/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/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/sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/_sphinx_javascript_frameworks_compat.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/_sphinx_javascript_frameworks_compat.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//_sphinx_javascript_frameworks_compat.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//_sphinx_javascript_frameworks_compat.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/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/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/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/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/copyright", found 1 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/run-unit-test", 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/README.rst", 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/sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/_sphinx_javascript_frameworks_compat.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/_sphinx_javascript_frameworks_compat.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//_sphinx_javascript_frameworks_compat.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//_sphinx_javascript_frameworks_compat.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/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/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/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/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/user", found 13 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/partitioning-big-data.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/install.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/guide.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/galaxy.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/choosing-table-sizes.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/biblio.html", found 1 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/searchindex.js", 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/roadmap.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-2.1.html", found 1 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-1.4.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-1.2.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/release-1.0.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/index.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/introduction.html", 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/genindex.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/scripts-and-sandbox.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/python-api.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/hackathon.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/codebase-guide.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/a-quick-guide-to-testing.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/contributors.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/sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/_sphinx_javascript_frameworks_compat.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/_sphinx_javascript_frameworks_compat.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//_sphinx_javascript_frameworks_compat.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//_sphinx_javascript_frameworks_compat.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/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/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/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/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/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/sphinx_highlight.js"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js , found 0 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/pygments.css", found 1 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/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/labibi.js", found 1 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/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/jquery.min.js", 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/guzzle.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/source-serif-pro", found 35 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/bower.json", 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-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-Regular.ttf.woff", found 1 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-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-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-Black.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-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-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-Light.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-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-Black.otf.woff", 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-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-Light.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-Bold.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/SourceSerifProReadMe.html", found 1 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/README.md", 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-Semibold.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-Light.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-Bold.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/EOT", found 6 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/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-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-Black.eot", 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-SemiboldItalic-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-SemiboldItalic-webfont.svg", 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-Semibold-webfont.woff", 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-Semibold-webfont.svg", 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/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-Regular-webfont.ttf", 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-Regular-webfont.eot", 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-LightItalic-webfont.ttf", 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-LightItalic-webfont.eot", 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-Light-webfont.ttf", 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.eot", 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-Italic-webfont.ttf", 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-Italic-webfont.eot", 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-ExtraBoldItalic-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-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-ExtraBold-webfont.ttf", 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-ExtraBold-webfont.eot", 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-BoldItalic-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-BoldItalic-webfont.eot", 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-Bold-webfont.ttf", 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-Bold-webfont.eot", 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/glyphicons-halflings-regular.woff", found 1 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.svg", 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/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/LiberationSans-Italic.ttf", 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/documentation_options.js", 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/css", found 3 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/css/bootstrap-theme.min.css", 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/_sphinx_javascript_frameworks_compat.js"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//_sphinx_javascript_frameworks_compat.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//_sphinx_javascript_frameworks_compat.js , found 0 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/user", found 13 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/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/user/index.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/getting-help.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/examples.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/blog-posts.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/api-examples.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/_sources/release-notes", found 9 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-2.0.rst.txt", found 1 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-1.3.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-1.1.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-1.0.1.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/introduction.rst.txt", found 1 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/dev", found 13 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/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/index.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/guidelines-continued-dev.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/for-khmer-developers.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/binary-file-formats.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/CODE_OF_CONDUCT.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/LICENSE.rst.txt", 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/LICENSE.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/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 11892944 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 '/build/khmer-3.0.0~a3+dfsg' dh_installchangelogs -O--buildsystem=pybuild install -m0755 -d debian/liboxli1/usr/share/doc/liboxli1 install -p -m0644 debian/.debhelper/generated/liboxli1/dh_installchangelogs.dch.trimmed debian/liboxli1/usr/share/doc/liboxli1/changelog.Debian install -p -m0644 ./CHANGELOG.md debian/liboxli1/usr/share/doc/liboxli1/changelog install -m0755 -d debian/khmer/usr/share/doc/khmer install -p -m0644 debian/.debhelper/generated/khmer/dh_installchangelogs.dch.trimmed debian/khmer/usr/share/doc/khmer/changelog.Debian install -p -m0644 ./CHANGELOG.md debian/khmer/usr/share/doc/khmer/changelog install -m0755 -d debian/liboxli-dev/usr/share/doc/liboxli-dev install -p -m0644 debian/.debhelper/generated/liboxli-dev/dh_installchangelogs.dch.trimmed debian/liboxli-dev/usr/share/doc/liboxli-dev/changelog.Debian install -p -m0644 ./CHANGELOG.md debian/liboxli-dev/usr/share/doc/liboxli-dev/changelog install -m0755 -d debian/khmer-common/usr/share/doc/khmer-common install -p -m0644 debian/.debhelper/generated/khmer-common/dh_installchangelogs.dch.trimmed debian/khmer-common/usr/share/doc/khmer-common/changelog.Debian install -p -m0644 ./CHANGELOG.md debian/khmer-common/usr/share/doc/khmer-common/changelog dh_installman -O--buildsystem=pybuild install -m0755 -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_python3:179: version: 5.20230130 D: dh_python3 dh_python3:180: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:181: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, package=None, no_package=None, remaining_packages=False, 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_python3:182: supported Python versions: 3.11 (default=3.11) D: dh_python3 debhelper:175: skipping package khmer-common (missing ${python3:Depends} in Depends/Recommends) D: dh_python3 debhelper:175: skipping package liboxli1 (missing ${python3:Depends} in Depends/Recommends) D: dh_python3 debhelper:175: skipping package liboxli-dev (missing ${python3:Depends} in Depends/Recommends) D: dh_python3 debhelper:183: source=khmer, binary packages=['khmer'] D: dh_python3 dh_python3:204: processing package khmer... D: dh_python3 fs:52: moving files from debian/khmer/usr/lib/python3.11/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:400: package khmer details = {'requires.txt': {'debian/khmer/usr/lib/python3/dist-packages/khmer-3.0.0a3.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('3.11')}, 'ext_no_version': set()} D: dh_python3 depends:117: generating dependencies for package khmer D: dh_python3 pydist:173: trying to find dependency for screed>=1.0 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for argparse>=1.2.1 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:218: dependency: requirement already has hardcoded version D: dh_python3 depends:281: D={'python3 (<< 3.12)', 'python3-screed', 'python3 (>= 3.11~)', 'python3 (>= 3.2) | python3 (<< 2.6) | python3 (>> 2.7)', 'python3:any'}; R=[]; S=[]; E=[], B=[]; RT=[('/usr/lib/khmer', '')] dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild install -m0755 -d debian/khmer/usr/share/lintian/overrides install -p -m0644 debian/khmer.lintian-overrides debian/khmer/usr/share/lintian/overrides/khmer install -m0755 -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/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/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/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-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-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-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.woff ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.woff ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.woff 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.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-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-LightItalic-webfont.woff ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.woff 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-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.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-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-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-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-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-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-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-Bold-webfont.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Bold-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-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-ExtraBoldItalic-webfont.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.ttf 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-LightItalic-webfont.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.ttf 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-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-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-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-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-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.svg ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Bold-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.svg 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-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-Regular-webfont.svg ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Regular-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.svg rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.svg ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.svg 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-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-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-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/stylesheet.css ln -s ../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/stylesheet.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/stylesheet.css rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Black.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/EOT/SourceSerifPro-Black.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Black.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Regular.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/EOT/SourceSerifPro-Regular.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Regular.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-ExtraLight.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/EOT/SourceSerifPro-ExtraLight.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-ExtraLight.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Light.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/EOT/SourceSerifPro-Light.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Light.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Semibold.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/EOT/SourceSerifPro-Semibold.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Semibold.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Bold.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/EOT/SourceSerifPro-Bold.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Bold.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-ExtraLight.otf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/OTF/SourceSerifPro-ExtraLight.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-ExtraLight.otf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Black.otf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/OTF/SourceSerifPro-Black.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Black.otf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Regular.otf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/OTF/SourceSerifPro-Regular.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Regular.otf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Light.otf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/OTF/SourceSerifPro-Light.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Light.otf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Bold.otf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/OTF/SourceSerifPro-Bold.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Bold.otf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Semibold.otf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/OTF/SourceSerifPro-Semibold.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Semibold.otf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Black.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/TTF/SourceSerifPro-Black.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Black.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-ExtraLight.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/TTF/SourceSerifPro-ExtraLight.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-ExtraLight.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Regular.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/TTF/SourceSerifPro-Regular.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Regular.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Light.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/TTF/SourceSerifPro-Light.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Light.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Semibold.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/TTF/SourceSerifPro-Semibold.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Semibold.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Bold.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/TTF/SourceSerifPro-Bold.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Bold.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-ExtraLight.otf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-ExtraLight.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-ExtraLight.otf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Black.otf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Black.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Black.otf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Regular.otf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Regular.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Regular.otf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Light.otf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Light.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Light.otf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Bold.otf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Bold.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Bold.otf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Semibold.otf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Semibold.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Semibold.otf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-ExtraLight.ttf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-ExtraLight.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-ExtraLight.ttf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Black.ttf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Black.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Black.ttf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Regular.ttf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Regular.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Regular.ttf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Light.ttf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Light.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Light.ttf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Semibold.ttf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Semibold.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Semibold.ttf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Bold.ttf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Bold.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Bold.ttf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/bower.json ln -s ../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/bower.json debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/bower.json rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/README.md ln -s ../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README.md debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/README.md rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/source-serif-pro.css ln -s ../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/source-serif-pro.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/source-serif-pro.css rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/ReadMe.html ln -s ../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/ReadMe.html debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/ReadMe.html rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/SourceSerifProReadMe.html ln -s ../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/SourceSerifProReadMe.html debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/SourceSerifProReadMe.html rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.woff2 ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/glyphicons-halflings-regular.woff2 debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.woff2 rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.eot ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/glyphicons-halflings-regular.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.woff ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/glyphicons-halflings-regular.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.woff rm -f 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/fonts/glyphicons-halflings-regular.svg ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/glyphicons-halflings-regular.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.svg rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSans-Regular.ttf ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/LiberationSans-Regular.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSans-Regular.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSerif-Regular.ttf ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/LiberationSerif-Regular.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSerif-Regular.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSans-Italic.ttf ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/LiberationSans-Italic.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSans-Italic.ttf 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/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/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/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/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.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/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/_sphinx_javascript_frameworks_compat.js ln -s ../../../../javascript/sphinxdoc/1.0/_sphinx_javascript_frameworks_compat.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/_sphinx_javascript_frameworks_compat.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js ln -s ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.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/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 1664033683 as canonical time 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/_static/plus.png using File::StripNondeterminism::handlers::png 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/_images/partitioning-workflow.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 Using 1664033683 as canonical time 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/random-20-a.fq.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fa.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/goodversion-k12.ht.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-reads.fq.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 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/liboxli-dev/changelog usr/share/doc/liboxli-dev/changelog.Debian chmod a-x usr/share/doc/khmer/changelog usr/share/doc/khmer/changelog.Debian usr/share/man/man1/khmer.1 chmod a-x usr/share/doc/liboxli1/changelog usr/share/doc/liboxli1/changelog.Debian gzip -9nf usr/share/doc/khmer/changelog usr/share/doc/khmer/changelog.Debian usr/share/man/man1/khmer.1 gzip -9nf usr/share/doc/liboxli-dev/changelog usr/share/doc/liboxli-dev/changelog.Debian chmod a-x usr/share/doc/khmer-common/CITATION usr/share/doc/khmer-common/changelog usr/share/doc/khmer-common/changelog.Debian gzip -9nf usr/share/doc/liboxli1/changelog usr/share/doc/liboxli1/changelog.Debian cd '/build/khmer-3.0.0~a3+dfsg' cd '/build/khmer-3.0.0~a3+dfsg' gzip -9nf usr/share/doc/khmer-common/CITATION usr/share/doc/khmer-common/changelog usr/share/doc/khmer-common/changelog.Debian cd '/build/khmer-3.0.0~a3+dfsg' cd '/build/khmer-3.0.0~a3+dfsg' 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/liboxli-dev ! -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/khmer-common ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/liboxli-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/liboxli-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/khmer/usr/share/doc -type f -a -true -a ! -regex 'debian/khmer/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli1/usr/share/doc -type f -a -true -a ! -regex 'debian/liboxli1/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/liboxli-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/khmer/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/liboxli1/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/liboxli-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/khmer-common/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 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/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/liboxli1/usr/share/lintian/overrides -type f -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/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/liboxli1 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/khmer/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/liboxli1/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 -m0755 -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-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashset.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hllcounter.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so objcopy --compress-debug-sections debian/khmer/usr/lib/debug/.dwz/x86_64-linux-gnu/khmer.debug chmod 0644 -- debian/khmer/usr/lib/debug/.dwz/x86_64-linux-gnu/khmer.debug dh_strip -a -O--buildsystem=pybuild strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives -R .gnu.lto_\* -R .gnu.debuglto_\* -N __gnu_lto_slim -N __gnu_lto_v1 debian/liboxli-dev/usr/lib/x86_64-linux-gnu/liboxli.a install -m0755 -d debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/e9 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/e9/f99a6115cdf7b8cb206a535bd94db451923e2b.debug install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/2c objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-311-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/2c/a46e847f722fd2d6bb095b169de947522a48d1.debug chmod 0644 -- debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/e9/f99a6115cdf7b8cb206a535bd94db451923e2b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded 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/e9/f99a6115cdf7b8cb206a535bd94db451923e2b.debug debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 install -m0755 -d debian/.debhelper/liboxli1/dbgsym-root/usr/share/doc ln -s liboxli1 debian/.debhelper/liboxli1/dbgsym-root/usr/share/doc/liboxli1-dbgsym install -m0755 -d debian/.debhelper/liboxli1 chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/2c/a46e847f722fd2d6bb095b169de947522a48d1.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/2c/a46e847f722fd2d6bb095b169de947522a48d1.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/3b objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/3b/70e0e8a6991ee9661df1e8455074a3ba39dbd8.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/3b/70e0e8a6991ee9661df1e8455074a3ba39dbd8.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/3b/70e0e8a6991ee9661df1e8455074a3ba39dbd8.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/2b objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/2b/c2c8cb62716a4be2aa0a378a7433a6416f3dba.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/2b/c2c8cb62716a4be2aa0a378a7433a6416f3dba.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/2b/c2c8cb62716a4be2aa0a378a7433a6416f3dba.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/74 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/74/9abd8fd5e17166c2096af468f92497dcec9661.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/74/9abd8fd5e17166c2096af468f92497dcec9661.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/74/9abd8fd5e17166c2096af468f92497dcec9661.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/a1 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-311-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/a1/8f3ea34a8ff4fec9afc3cc5a140f0ffefbeff9.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/a1/8f3ea34a8ff4fec9afc3cc5a140f0ffefbeff9.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/a1/8f3ea34a8ff4fec9afc3cc5a140f0ffefbeff9.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/19 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/19/3454b199c4dcc17fd129ad09a1b5dc88f7f3c9.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/19/3454b199c4dcc17fd129ad09a1b5dc88f7f3c9.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/19/3454b199c4dcc17fd129ad09a1b5dc88f7f3c9.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/5d objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/5d/0b49282ba04ea1d846bbb432a1f505e621f3be.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/5d/0b49282ba04ea1d846bbb432a1f505e621f3be.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/5d/0b49282ba04ea1d846bbb432a1f505e621f3be.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/31 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/31/ff7b1d8f26003b946ecbc3da85dcafc0bc0a3c.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/31/ff7b1d8f26003b946ecbc3da85dcafc0bc0a3c.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/31/ff7b1d8f26003b946ecbc3da85dcafc0bc0a3c.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/b6 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-311-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/b6/6d284b42d9ba721d4f7d77d1d2cd66c1642b54.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/b6/6d284b42d9ba721d4f7d77d1d2cd66c1642b54.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/b6/6d284b42d9ba721d4f7d77d1d2cd66c1642b54.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/87 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hllcounter.cpython-311-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/87/991e96e7c3c47e7859149bed9d42314fc3504a.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/87/991e96e7c3c47e7859149bed9d42314fc3504a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hllcounter.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/87/991e96e7c3c47e7859149bed9d42314fc3504a.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hllcounter.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/18 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashset.cpython-311-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/18/ac51430420264e6b959c600e3d15846d27145d.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/18/ac51430420264e6b959c600e3d15846d27145d.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashset.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/18/ac51430420264e6b959c600e3d15846d27145d.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashset.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/2a objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/2a/305e674cb582a018c09d7a780d10079818100b.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/2a/305e674cb582a018c09d7a780d10079818100b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/2a/305e674cb582a018c09d7a780d10079818100b.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so install -m0755 -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 -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/share/doc ln -s khmer debian/.debhelper/khmer/dbgsym-root/usr/share/doc/khmer-dbgsym install -m0755 -d debian/.debhelper/khmer dh_makeshlibs -a -O--buildsystem=pybuild rm -f debian/khmer/DEBIAN/shlibs rm -f debian/liboxli1/DEBIAN/shlibs install -m0755 -d debian/liboxli1/DEBIAN echo "liboxli 1 liboxli1 (>= 3.0.0~a3+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 install -m0755 -d debian/liboxli1/DEBIAN dpkg-shlibdeps -Tdebian/liboxli1.substvars debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 install -m0755 -d debian/khmer/DEBIAN dpkg-shlibdeps -Tdebian/khmer.substvars debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hllcounter.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashset.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so dpkg-shlibdeps: warning: symbol BZ2_bzWriteOpen used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzopen64 used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol BZ2_bzWriteClose used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzerror used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol inflateEnd 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 inflate used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzopen used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol deflateInit2_ used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzclearerr 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 -m0755 -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 install -m0755 -d debian/khmer/DEBIAN 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 -m0755 -d debian/liboxli1/DEBIAN install -p -m0644 debian/.debhelper/generated/liboxli1/triggers debian/liboxli1/DEBIAN/triggers install -m0755 -d debian/liboxli-dev/DEBIAN dh_gencontrol -O--buildsystem=pybuild install -m0755 -d debian/khmer-common/DEBIAN 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 install -m0755 -d debian/khmer/DEBIAN echo misc:Depends= >> debian/khmer.substvars echo misc:Pre-Depends= >> debian/khmer.substvars install -m0755 -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=18ac51430420264e6b959c600e3d15846d27145d 193454b199c4dcc17fd129ad09a1b5dc88f7f3c9 2a305e674cb582a018c09d7a780d10079818100b 2bc2c8cb62716a4be2aa0a378a7433a6416f3dba 2ca46e847f722fd2d6bb095b169de947522a48d1 31ff7b1d8f26003b946ecbc3da85dcafc0bc0a3c 3b70e0e8a6991ee9661df1e8455074a3ba39dbd8 5d0b49282ba04ea1d846bbb432a1f505e621f3be 749abd8fd5e17166c2096af468f92497dcec9661 87991e96e7c3c47e7859149bed9d42314fc3504a a18f3ea34a8ff4fec9afc3cc5a140f0ffefbeff9 b66d284b42d9ba721d4f7d77d1d2cd66c1642b54" -DSection=debug -UMulti-Arch -UReplaces -UBreaks install -m0755 -d debian/liboxli1/DEBIAN echo misc:Depends= >> debian/liboxli1.substvars echo misc:Pre-Depends= >> debian/liboxli1.substvars install -m0755 -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=e9f99a6115cdf7b8cb206a535bd94db451923e2b -DSection=debug -UReplaces -UBreaks install -m0755 -d debian/liboxli-dev/DEBIAN 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 chmod 0644 -- debian/.debhelper/liboxli1/dbgsym-root/DEBIAN/control dpkg-gencontrol -pliboxli1 -ldebian/changelog -Tdebian/liboxli1.substvars -Pdebian/liboxli1 chmod 0644 -- debian/khmer-common/DEBIAN/control chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/DEBIAN/control dpkg-gencontrol -pkhmer -ldebian/changelog -Tdebian/khmer.substvars -Pdebian/khmer chmod 0644 -- debian/liboxli-dev/DEBIAN/control chmod 0644 -- debian/liboxli1/DEBIAN/control chmod 0644 -- debian/khmer/DEBIAN/control dh_md5sums -O--buildsystem=pybuild install -m0755 -d debian/khmer-common/DEBIAN install -m0755 -d debian/liboxli1/DEBIAN install -m0755 -d debian/liboxli-dev/DEBIAN install -m0755 -d debian/khmer/DEBIAN cd debian/liboxli1 >/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 cd debian/khmer >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/liboxli-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/liboxli1/DEBIAN/md5sums install -m0755 -d debian/.debhelper/liboxli1/dbgsym-root/DEBIAN chmod 0644 -- debian/khmer-common/DEBIAN/md5sums cd debian/.debhelper/liboxli1/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/liboxli-dev/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/liboxli1/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/khmer/DEBIAN/md5sums install -m0755 -d debian/.debhelper/khmer/dbgsym-root/DEBIAN 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 .. dpkg-deb --root-owner-group --build debian/liboxli1 .. dpkg-deb --root-owner-group --build debian/.debhelper/liboxli1/dbgsym-root .. dpkg-deb --root-owner-group --build debian/.debhelper/khmer/dbgsym-root .. dpkg-deb --root-owner-group --build debian/khmer .. dpkg-deb: building package 'khmer-common' in '../khmer-common_3.0.0~a3+dfsg-4_all.deb'. dpkg-deb --root-owner-group --build debian/liboxli-dev .. dpkg-deb: building package 'liboxli1' in '../liboxli1_3.0.0~a3+dfsg-4_amd64.deb'. dpkg-deb: building package 'liboxli-dev' in '../liboxli-dev_3.0.0~a3+dfsg-4_amd64.deb'. dpkg-deb: building package 'khmer-dbgsym' in '../khmer-dbgsym_3.0.0~a3+dfsg-4_amd64.deb'. dpkg-deb: building package 'khmer' in '../khmer_3.0.0~a3+dfsg-4_amd64.deb'. dpkg-deb: building package 'liboxli1-dbgsym' in '../liboxli1-dbgsym_3.0.0~a3+dfsg-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../khmer_3.0.0~a3+dfsg-4_amd64.buildinfo dpkg-genchanges --build=binary -O../khmer_3.0.0~a3+dfsg-4_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) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3152983/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3152983/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3152983 and its subdirectories I: Current time: Thu Jun 8 00:38:27 +14 2023 I: pbuilder-time-stamp: 1686134307