I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 4 11:53:33 +14 2024 I: pbuilder-time-stamp: 1725400413 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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_2.1.2+dfsg-8.dsc] I: copying [./khmer_2.1.2+dfsg.orig.tar.gz] I: copying [./khmer_2.1.2+dfsg-8.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.rFLLeSpT/trustedkeys.kbx': General error gpgv: Signature made Tue Jan 5 03:34:45 2021 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./khmer_2.1.2+dfsg-8.dsc dpkg-source: info: extracting khmer in khmer-2.1.2+dfsg dpkg-source: info: unpacking khmer_2.1.2+dfsg.orig.tar.gz dpkg-source: info: unpacking khmer_2.1.2+dfsg-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying update-manifest dpkg-source: info: applying setup-py-py3 dpkg-source: info: applying local-libs dpkg-source: info: applying older-setuptools dpkg-source: info: applying disable_google_analytics dpkg-source: info: applying get_version dpkg-source: info: applying install-prefix dpkg-source: info: applying cpython-bug-empty-exceptions dpkg-source: info: applying amend-skip dpkg-source: info: applying setup.py-py3 dpkg-source: info: applying python3 dpkg-source: info: applying fix_liboxli_test I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/147165/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-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 Sep 4 11:53 /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/147165/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/147165/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.1.4(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,-fixfilepath parallel=16 ' DIRSTACK=() DISTRIBUTION=bullseye EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=f37432a716d64206b862fa731f1f43ad 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=147165 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.G2m1RxD3/pbuilderrc_DUtG --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.G2m1RxD3/b2 --logfile b2/build.log khmer_2.1.2+dfsg-8.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://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.38-2 (2023-07-27) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jan 21 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 69032 Jan 21 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 203072 Jan 25 2023 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 98048 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 8 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jan 21 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 21 2022 more -rwsr-xr-x 1 root root 55528 Jan 21 2022 mount -rwxr-xr-x 1 root root 18664 Jan 21 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 9 Sep 4 11:53 sh -> /bin/bash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jan 21 2022 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 21 2022 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 21 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 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 5898 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 8049 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/147165/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 (>= 1.0), python3-pytest, python3-pytest-runner, python3-sphinx, python3-sphinxcontrib.autoprogram, cython3 (>= 0.26.1), 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 ... 19707 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 (>= 1.0); 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 (>= 0.26.1); 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} libicu67{a} libjs-bootstrap{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmpdec3{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.9{a} libpython3.9-dev{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} libruby2.7{a} libsigsegv2{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-bz2file{a} python3-certifi{a} python3-chardet{a} python3-dev{a} python3-distutils{a} python3-docutils{a} python3-guzzle-sphinx-theme{a} python3-idna{a} python3-imagesize{a} python3-importlib-metadata{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-pyparsing{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-toml{a} python3-tz{a} python3-urllib3{a} python3-zipp{a} python3.9{a} python3.9-dev{a} python3.9-minimal{a} rake{a} rdfind{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-rubygems{a} ruby-test-unit{a} ruby-xmlrpc{a} ruby2.7{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 libltdl-dev libmail-sendmail-perl libpaper-utils lynx python3-pil wget zip 0 packages upgraded, 125 newly installed, 0 to remove and 0 not upgraded. Need to get 51.7 MB of archives. After unpacking 208 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 sgml-base all 1.30 [15.1 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1n-0+deb11u4 [853 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 rubygems-integration all 1.18 [6704 B] Get: 27 http://deb.debian.org/debian bullseye/main amd64 rake all 13.0.3-1 [84.7 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 ruby-minitest all 5.13.0-1 [57.3 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 ruby-power-assert all 1.1.7-2 [11.5 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 ruby-test-unit all 3.3.9-1 [86.1 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libedit2 amd64 3.1-20191231-2+b1 [96.7 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libruby2.7 amd64 2.7.4-1+deb11u1 [4202 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 ruby2.7 amd64 2.7.4-1+deb11u1 [747 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 ruby-rubygems all 3.2.5-2 [281 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 ruby amd64 1:2.7+2 [11.7 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 ruby-asciidoctor all 2.0.12-2 [206 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 asciidoctor all 2.0.12-2 [83.9 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 cython3 amd64 0.29.21-3+b1 [1312 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 dh-exec amd64 0.23.2 [26.6 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 python3-distutils all 3.9.2-1 [143 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 docutils-common all 0.16+dfsg-4 [129 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-2 [164 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 fonts-liberation all 1:1.07.4-11 [828 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libbz2-dev amd64 1.0.8-4 [30.1 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libexpat1-dev amd64 2.2.10-2+deb11u5 [141 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libjs-bootstrap all 3.4.1+dfsg-2 [173 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libpython3.9 amd64 3.9.2-1 [1691 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-dev amd64 3.9.2-1 [4028 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 libpython3-dev amd64 3.9.2-3 [21.7 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 libpython3-all-dev amd64 3.9.2-3 [1068 B] Get: 83 http://deb.debian.org/debian bullseye/main amd64 python-babel-localedata all 2.8.0+dfsg.1-7 [4997 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 python3-alabaster all 0.7.8-1.1 [18.6 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 python3-all amd64 3.9.2-3 [1056 B] Get: 86 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 python3.9-dev amd64 3.9.2-1 [515 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 python3-dev amd64 3.9.2-3 [24.8 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 python3-all-dev amd64 3.9.2-3 [1064 B] Get: 90 http://deb.debian.org/debian bullseye/main amd64 python3-attr all 20.3.0-1 [52.9 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 python3-tz all 2021.1-1 [34.8 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 python3-babel all 2.8.0+dfsg.1-7 [100 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 python3-bz2file all 0.98-3 [8012 B] Get: 95 http://deb.debian.org/debian bullseye/main amd64 python3-certifi all 2020.6.20-1 [151 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 python3-chardet all 4.0.0-1 [99.0 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 python3-roman all 2.0.0-5 [9064 B] Get: 98 http://deb.debian.org/debian bullseye/main amd64 python3-docutils all 0.16+dfsg-4 [384 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 sphinx-common all 3.4.3-2 [578 kB] Get: 100 http://deb.debian.org/debian bullseye/main amd64 python3-imagesize all 1.2.0-2 [5824 B] Get: 101 http://deb.debian.org/debian bullseye/main amd64 python3-markupsafe amd64 1.1.1-1+b3 [15.2 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 python3-jinja2 all 2.11.3-1 [114 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 python3-pyparsing all 2.4.7-1 [109 kB] Get: 104 http://deb.debian.org/debian bullseye/main amd64 python3-packaging all 20.9-2 [33.5 kB] Get: 105 http://deb.debian.org/debian bullseye/main amd64 python3-pygments all 2.7.1+dfsg-2.1 [657 kB] Get: 106 http://deb.debian.org/debian bullseye/main amd64 python3-idna all 2.10-1 [37.4 kB] Get: 107 http://deb.debian.org/debian bullseye/main amd64 python3-six all 1.16.0-2 [17.5 kB] Get: 108 http://deb.debian.org/debian bullseye/main amd64 python3-urllib3 all 1.26.5-1~exp1 [114 kB] Get: 109 http://deb.debian.org/debian bullseye/main amd64 python3-requests all 2.25.1+dfsg-2 [69.3 kB] Get: 110 http://deb.debian.org/debian bullseye/main amd64 python3-snowballstemmer all 2.1.0-1 [58.7 kB] Get: 111 http://deb.debian.org/debian bullseye/main amd64 python3-sphinx all 3.4.3-2 [545 kB] Get: 112 http://deb.debian.org/debian bullseye/main amd64 python3-guzzle-sphinx-theme all 0.7.11-5 [1346 kB] Get: 113 http://deb.debian.org/debian bullseye/main amd64 python3-more-itertools all 4.2.0-3 [42.7 kB] Get: 114 http://deb.debian.org/debian bullseye/main amd64 python3-zipp all 1.0.0-3 [6060 B] Get: 115 http://deb.debian.org/debian bullseye/main amd64 python3-importlib-metadata all 1.6.0-2 [10.3 kB] Get: 116 http://deb.debian.org/debian bullseye/main amd64 python3-iniconfig all 1.1.1-1 [6308 B] Get: 117 http://deb.debian.org/debian bullseye/main amd64 python3-pluggy all 0.13.0-6 [22.3 kB] Get: 118 http://deb.debian.org/debian bullseye/main amd64 python3-py all 1.10.0-1 [94.2 kB] Get: 119 http://deb.debian.org/debian bullseye/main amd64 python3-toml all 0.10.1-1 [15.9 kB] Get: 120 http://deb.debian.org/debian bullseye/main amd64 python3-pytest all 6.0.2-2 [211 kB] Get: 121 http://deb.debian.org/debian bullseye/main amd64 python3-setuptools all 52.0.0-4 [366 kB] Get: 122 http://deb.debian.org/debian bullseye/main amd64 python3-pytest-runner all 2.11.1-1.2 [8528 B] Get: 123 http://deb.debian.org/debian bullseye/main amd64 python3-screed all 1.0.5-1 [109 kB] Get: 124 http://deb.debian.org/debian bullseye/main amd64 python3-sphinxcontrib.autoprogram all 0.1.5-2 [9692 B] Get: 125 http://deb.debian.org/debian bullseye/main amd64 rdfind amd64 1.4.1-1+b3 [40.7 kB] Fetched 51.7 MB in 1s (70.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19707 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. 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Setting up libexpat1:amd64 (2.2.10-2+deb11u5) ... Setting up python3.9-minimal (3.9.2-1) ... 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 ... 20574 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:amd64. Preparing to unpack .../2-libmpdec3_2.5.1-1_amd64.deb ... Unpacking libmpdec3:amd64 (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../4-libreadline8_8.1-1_amd64.deb ... Unpacking libreadline8:amd64 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:amd64. Preparing to unpack .../5-libpython3.9-stdlib_3.9.2-1_amd64.deb ... Unpacking libpython3.9-stdlib:amd64 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../6-python3.9_3.9.2-1_amd64.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../7-libpython3-stdlib_3.9.2-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... 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 ... 20995 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_amd64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.30_all.deb ... Unpacking sgml-base (1.30) ... 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Preparing to unpack .../008-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../009-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package rake. Preparing to unpack .../010-rake_13.0.3-1_all.deb ... Unpacking rake (13.0.3-1) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../011-ruby-minitest_5.13.0-1_all.deb ... Unpacking ruby-minitest (5.13.0-1) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../012-ruby-net-telnet_0.1.1-2_all.deb ... Unpacking ruby-net-telnet (0.1.1-2) ... Selecting previously unselected package ruby-power-assert. Preparing to unpack .../013-ruby-power-assert_1.1.7-2_all.deb ... Unpacking ruby-power-assert (1.1.7-2) ... Selecting previously unselected package ruby-test-unit. 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Preparing to unpack .../020-libruby2.7_2.7.4-1+deb11u1_amd64.deb ... Unpacking libruby2.7:amd64 (2.7.4-1+deb11u1) ... Selecting previously unselected package ruby2.7. Preparing to unpack .../021-ruby2.7_2.7.4-1+deb11u1_amd64.deb ... Unpacking ruby2.7 (2.7.4-1+deb11u1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../022-ruby-rubygems_3.2.5-2_all.deb ... Unpacking ruby-rubygems (3.2.5-2) ... Selecting previously unselected package ruby. Preparing to unpack .../023-ruby_1%3a2.7+2_amd64.deb ... Unpacking ruby (1:2.7+2) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../024-ruby-asciidoctor_2.0.12-2_all.deb ... Unpacking ruby-asciidoctor (2.0.12-2) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../025-asciidoctor_2.0.12-2_all.deb ... Unpacking asciidoctor (2.0.12-2) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../026-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../027-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../028-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../029-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../030-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../031-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package cython3. Preparing to unpack .../032-cython3_0.29.21-3+b1_amd64.deb ... Unpacking cython3 (0.29.21-3+b1) ... Selecting previously unselected package libdebhelper-perl. 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Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../039-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../040-libelf1_0.183-1_amd64.deb ... Unpacking libelf1:amd64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../041-dwz_0.13+20210201-1_amd64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../042-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../043-libxml2_2.9.10+dfsg-6.7+deb11u4_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Selecting previously unselected package gettext. Preparing to unpack .../044-gettext_0.21-4_amd64.deb ... Unpacking gettext (0.21-4) ... 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Selecting previously unselected package python3-setuptools. Preparing to unpack .../104-python3-setuptools_52.0.0-4_all.deb ... Unpacking python3-setuptools (52.0.0-4) ... Selecting previously unselected package python3-pytest-runner. Preparing to unpack .../105-python3-pytest-runner_2.11.1-1.2_all.deb ... Unpacking python3-pytest-runner (2.11.1-1.2) ... Selecting previously unselected package python3-screed. Preparing to unpack .../106-python3-screed_1.0.5-1_all.deb ... Unpacking python3-screed (1.0.5-1) ... Selecting previously unselected package python3-sphinxcontrib.autoprogram. Preparing to unpack .../107-python3-sphinxcontrib.autoprogram_0.1.5-2_all.deb ... Unpacking python3-sphinxcontrib.autoprogram (0.1.5-2) ... Selecting previously unselected package rdfind. Preparing to unpack .../108-rdfind_1.4.1-1+b3_amd64.deb ... Unpacking rdfind (1.4.1-1+b3) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:amd64 (1.5.3-1) ... Setting up bsdextrautils (2.36.1-8+deb11u1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-7) ... Setting up ruby-power-assert (1.1.7-2) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.2-1) ... Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-2) ... Setting up libdebhelper-perl (13.3.4) ... Setting up rdfind (1.4.1-1+b3) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up python-babel-localedata (2.8.0+dfsg.1-7) ... Setting up ruby-minitest (5.13.0-1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libexpat1-dev:amd64 (2.2.10-2+deb11u5) ... Setting up ruby-test-unit (3.3.9-1) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2+deb11u2) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up fonts-liberation (1:1.07.4-11) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up sgml-base (1.30) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up openssl (1.1.1n-0+deb11u4) ... Setting up libbsd0:amd64 (0.11.3-1) ... Setting up libelf1:amd64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up libjs-bootstrap (3.4.1+dfsg-2) ... Setting up libjs-underscore (1.9.1~dfsg-3) ... Setting up libbz2-dev:amd64 (1.0.8-4) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libedit2:amd64 (3.1-20191231-2+b1) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libjs-sphinxdoc (3.4.3-2) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up xml-core (0.18+nmu1) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up libpython3.9:amd64 (3.9.2-1) ... Setting up sphinx-common (3.4.3-2) ... Setting up python3.9 (3.9.2-1) ... Setting up libpython3.9-dev:amd64 (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up dh-exec (0.23.2) ... Setting up python3-markupsafe (1.1.1-1+b3) ... Setting up python3-tz (2021.1-1) ... Setting up python3-bz2file (0.98-3) ... Setting up python3-six (1.16.0-2) ... Setting up python3-roman (2.0.0-5) ... Setting up python3-jinja2 (2.11.3-1) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-certifi (2020.6.20-1) ... Setting up python3-snowballstemmer (2.1.0-1) ... Setting up python3-idna (2.10-1) ... Setting up cython3 (0.29.21-3+b1) ... Setting up python3-toml (0.10.1-1) ... Setting up python3-urllib3 (1.26.5-1~exp1) ... Setting up python3.9-dev (3.9.2-1) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-imagesize (1.2.0-2) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Setting up python3-more-itertools (4.2.0-3) ... Setting up python3-iniconfig (1.1.1-1) ... Setting up python3-attr (20.3.0-1) ... Setting up libpython3-dev:amd64 (3.9.2-3) ... Setting up python3-setuptools (52.0.0-4) ... Setting up python3-screed (1.0.5-1) ... Setting up python3-py (1.10.0-1) ... Setting up python3-babel (2.8.0+dfsg.1-7) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-alabaster (0.7.8-1.1) ... Setting up python3-all (3.9.2-3) ... Setting up python3-zipp (1.0.0-3) ... Setting up python3-pygments (2.7.1+dfsg-2.1) ... Setting up python3-packaging (20.9-2) ... Setting up python3-chardet (4.0.0-1) ... Setting up libpython3-all-dev:amd64 (3.9.2-3) ... Setting up python3-dev (3.9.2-3) ... Setting up python3-requests (2.25.1+dfsg-2) ... Setting up python3-pytest-runner (2.11.1-1.2) ... Setting up python3-all-dev (3.9.2-3) ... Setting up python3-importlib-metadata (1.6.0-2) ... Setting up python3-pluggy (0.13.0-6) ... Setting up python3-pytest (6.0.2-2) ... Setting up ruby2.7 (2.7.4-1+deb11u1) ... Setting up ruby-rubygems (3.2.5-2) ... Setting up ruby (1:2.7+2) ... Setting up ruby-asciidoctor (2.0.12-2) ... Setting up rake (13.0.3-1) ... Setting up asciidoctor (2.0.12-2) ... Setting up libruby2.7:amd64 (2.7.4-1+deb11u1) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... Processing triggers for sgml-base (1.30) ... Setting up docutils-common (0.16+dfsg-4) ... Processing triggers for sgml-base (1.30) ... Setting up python3-docutils (0.16+dfsg-4) ... update-alternatives: using /usr/share/docutils/scripts/python3/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up python3-sphinx (3.4.3-2) ... Setting up python3-guzzle-sphinx-theme (0.7.11-5) ... Setting up python3-sphinxcontrib.autoprogram (0.1.5-2) ... Processing triggers for ca-certificates (20210119) ... 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 I: Building the package I: user script /srv/workspace/pbuilder/147165/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bullseye I: user script /srv/workspace/pbuilder/147165/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/khmer-2.1.2+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_2.1.2+dfsg-8_source.changes dpkg-buildpackage: info: source package khmer dpkg-buildpackage: info: source version 2.1.2+dfsg-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe 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-2.1.2+dfsg' dh_auto_clean || /bin/true install -d /build/khmer-2.1.2\+dfsg/debian/.debhelper/generated/_source/home pybuild --clean --test-pytest -i python{version} -p 3.9 I: pybuild base:232: python3.9 setup.py clean running clean removing '/build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.9' 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-2.1.2+dfsg/src/oxli' rm -f *.o *.a *.so* oxli.pc make[2]: Leaving directory '/build/khmer-2.1.2+dfsg/src/oxli' rm -rf __pycache__ .eggs make[1]: Leaving directory '/build/khmer-2.1.2+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 debian/files rm -fr -- debian/khmer-common/ debian/tmp/ debian/khmer/ debian/liboxli1/ debian/liboxli-dev/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild install -d /build/khmer-2.1.2\+dfsg/debian/.debhelper/generated/_source/home pybuild --configure --test-pytest -i python{version} -p 3.9 I: pybuild base:232: python3.9 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/khmer-2.1.2+dfsg' dh_auto_build pybuild --build --test-pytest -i python{version} -p 3.9 I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_py creating /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/utils.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/trimming.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/thread_utils.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/khmer_logger.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/khmer_args.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/kfile.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/_version.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/__init__.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer creating /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/khmer_tst_utils.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_read_parsers.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_version.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_threaded_sequence_processor.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_tabletype.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_subset_graph.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_streaming_io.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_sequence_validation.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_scripts.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_script_output.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_script_arguments.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_sandbox_scripts.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_read_handling.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_read_aligner.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_oxli_functions.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_normalize_by_median.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_nodegraph.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_nibblestorage.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_lump.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_labelhash.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_hll.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_hashset.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_graph.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_functions.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_filter_abund.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_cython_parsing.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_cython_assembly.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_cpython_hierarchy.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_counttable.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_counting_single.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_countgraph.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_banding.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/graph_features.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/__init__.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests creating /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli copying oxli/partition.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli copying oxli/functions.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli copying oxli/build_graph.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli copying oxli/__init__.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli creating /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/__init__.py -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli running egg_info creating khmer.egg-info writing khmer.egg-info/PKG-INFO writing dependency_links to khmer.egg-info/dependency_links.txt writing requirements to khmer.egg-info/requires.txt writing top-level names to khmer.egg-info/top_level.txt writing manifest file 'khmer.egg-info/SOURCES.txt' reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.hh' under directory 'khmer' warning: no files found matching '*.cpp' under directory 'khmer/_oxli' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching '*.c' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '[Mm]akefile*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution writing manifest file 'khmer.egg-info/SOURCES.txt' copying tests/.gitignore -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests creating /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.bz2 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.gz -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.truncated.bz2 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.truncated.gz -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/README.rst -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/all-A.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k12.ct -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k12.ht -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k32.stoptags -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k32.tagset -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/banding-reads.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/biglump-random-20-a.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/bogus.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/casava_18-pe.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/combine_parts_1.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-all-paired-all-keep.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-none-paired.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-some-paired-all-keep.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file.bz2 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file.gz -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/fakelump.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/fakelump.fa.stoptags.txt -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/filter-test-A.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/filter-test-B.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k12.ht -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k12.ht.gz -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k32.stoptags -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k32.tagset -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/multi-output.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/normC20k20.ct -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/old-style-format-w-comments.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.1 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.2 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.badleft -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.badright -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.paired_bad -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken2.fq.1 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken2.fq.2 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken3.fq.1 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken3.fq.2 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken4.fq.1 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken4.fq.2 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-2.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-broken.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-witherror.fa.pe -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa.pe -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa.se -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq.pe -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq.se -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq.1 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq.2 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa.1 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa.2 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq.1 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq.2 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.malformat.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.malformat.fq.2 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired_one.base.dif.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-X2.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.even.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.bz2 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.gz -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.part -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq.bz2 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq.gz -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.odd.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-b.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-31-c.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/readaligner-default.json -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/readaligner-k12.json -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/real-partition-small.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/real-partition-tiny.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/simple-genome-reads.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/simple-genome.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/single-read.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/single-read.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa.bz2 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa.gz -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.paired.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.paired2.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-3.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-impaired.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-paired.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-paired.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-empty.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-empty.fa.bz2 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-error-reads.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-n-reads.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-reads.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-reads.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-filter-abund-Ns.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph2.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph5.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-labels.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-large.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-multi.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-output-partitions.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-overlap1.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-overlap2.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fq.bz2 -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fq.gz -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-short.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-contigs.fp -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-reads.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-reads.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-transcript.fa -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/truncated.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/unclean-reads.fastq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/valid-read-testing.fq -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying khmer/_oxli/assembly.pxd -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/assembly.pyx -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.pxd -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.pyx -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.pxd -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.pyx -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/hllcounter.pxd -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/oxli_types.pxd -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.pxd -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.pyx -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/traversal.pxd -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/utils.pxd -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/utils.pyx -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli UPDATING /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_version.py set /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_version.py to '2.1.2' running build_ext cythoning khmer/_oxli/utils.pyx to khmer/_oxli/utils.cpp /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/khmer-2.1.2+dfsg/khmer/_oxli/utils.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning khmer/_oxli/parsing.pyx to khmer/_oxli/parsing.cpp /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/khmer-2.1.2+dfsg/khmer/_oxli/parsing.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: khmer/_oxli/parsing.pxd:159:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:161:34: Declarations should not be declared inline. cythoning khmer/_oxli/hashing.pyx to khmer/_oxli/hashing.cpp /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/khmer-2.1.2+dfsg/khmer/_oxli/hashing.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning khmer/_oxli/graphs.pyx to khmer/_oxli/graphs.cpp /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/khmer-2.1.2+dfsg/khmer/_oxli/graphs.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: khmer/_oxli/parsing.pxd:159:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:161:34: Declarations should not be declared inline. cythoning khmer/_oxli/assembly.pyx to khmer/_oxli/assembly.cpp /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/khmer-2.1.2+dfsg/khmer/_oxli/assembly.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: khmer/_oxli/parsing.pxd:159:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:161:34: Declarations should not be declared inline. building 'khmer._khmer' extension creating build creating build/temp.linux-x86_64-3.9 creating build/temp.linux-x86_64-3.9/src creating build/temp.linux-x86_64-3.9/src/khmer creating build/temp.linux-x86_64-3.9/src/oxli creating build/temp.linux-x86_64-3.9/third-party creating build/temp.linux-x86_64-3.9/third-party/smhasher x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_countgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_counttable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_graphlabels.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashset.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashtable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hllcounter.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_nodegraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_nodetable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_readaligner.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_smallcountgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_smallcounttable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_subsetpartition.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-3.9/src/oxli/assembler.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor 'oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)': include/oxli/assembler.hh:80:23: warning: 'oxli::LinearAssembler::graph' will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ include/oxli/assembler.hh:79:16: warning: 'oxli::WordLength oxli::LinearAssembler::_ksize' [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor 'oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()': src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type 'oxli::LinearAssembler' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38: 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) : | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38: 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 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]': src/oxli/hashtable.cc:512:1: required from here src/oxli/hashtable.cc:103:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 103 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]': src/oxli/hashtable.cc:529:1: required from here src/oxli/hashtable.cc:133:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 133 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hllcounter.cc: In instantiation of 'void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]': src/oxli/hllcounter.cc:524:1: required from here src/oxli/hllcounter.cc:428:40: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 428 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o -O3 -std=c++11 -pedantic -fopenmp In file included from third-party/seqan/core/include/seqan/basic.h:62, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:116, 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, from src/oxli/read_parsers.cc:39: 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, 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, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function 'int seqan::_globalAlignmentScore(const seqan::String&, const seqan::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:74:2: 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, 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, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function 'seqan::Pair > seqan::_alignBandedSmithWatermanTrace(seqan::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:412:2: 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, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: 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 [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/store/store_all.h: In function 'void seqan::convertMatchesToGlobalAlignment(seqan::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:1737:2: 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 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/storage.cc -o build/temp.linux-x86_64-3.9/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/subset.cc -o build/temp.linux-x86_64-3.9/src/oxli/subset.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/subset.cc: In member function 'size_t oxli::SubsetPartition::output_partitioned_file(const string&, const 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 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-3.9/src/oxli/traversal.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:203:31: 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, | ^~~~~~~~~~~~~~~~~~~~~~~ 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 = true; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:203:31: 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 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_khmer.cpython-39-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.utils' extension creating build/temp.linux-x86_64-3.9/khmer creating build/temp.linux-x86_64-3.9/khmer/_oxli x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c khmer/_oxli/utils.cpp -o build/temp.linux-x86_64-3.9/khmer/_oxli/utils.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/khmer/_oxli/utils.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.parsing' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c khmer/_oxli/parsing.cpp -o build/temp.linux-x86_64-3.9/khmer/_oxli/parsing.o -O3 -std=c++11 -pedantic -fopenmp In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from khmer/_oxli/parsing.cpp:4: khmer/_oxli/parsing.cpp: In function 'PyObject* __pyx_pf_5khmer_5_oxli_7parsing_9Alphabets_get(PyObject*)': /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:2339:47: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 2339 | __pyx_t_4 = (__pyx_v_alphabet != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_alphabet) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: 'Py_UNICODE* PyUnicode_AsUnicode(PyObject*)' is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:2339:47: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 2339 | __pyx_t_4 = (__pyx_v_alphabet != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_alphabet) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:2339:47: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 2339 | __pyx_t_4 = (__pyx_v_alphabet != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_alphabet) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function 'PyObject* __pyx_pf_5khmer_5_oxli_7parsing_8Sequence_4name___get__(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*)': /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:3969:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 3969 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_name) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: 'Py_UNICODE* PyUnicode_AsUnicode(PyObject*)' is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:3969:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 3969 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_name) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:3969:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 3969 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_name) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function 'PyObject* __pyx_pf_5khmer_5_oxli_7parsing_8Sequence_8sequence___get__(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*)': /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4057:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4057 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_sequence) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: 'Py_UNICODE* PyUnicode_AsUnicode(PyObject*)' is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4057:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4057 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_sequence) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4057:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4057 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_sequence) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function 'PyObject* __pyx_pf_5khmer_5_oxli_7parsing_8Sequence_11description___get__(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*)': /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4144:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4144 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_description) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: 'Py_UNICODE* PyUnicode_AsUnicode(PyObject*)' is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4144:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4144 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_description) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4144:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4144 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_description) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function 'PyObject* __pyx_pf_5khmer_5_oxli_7parsing_8Sequence_7quality___get__(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*)': /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4228:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4228 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_quality) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: 'Py_UNICODE* PyUnicode_AsUnicode(PyObject*)' is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4228:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4228 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_quality) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4228:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4228 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_quality) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function 'PyObject* __pyx_pf_5khmer_5_oxli_7parsing_8Sequence_11cleaned_seq___get__(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*)': /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4312:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4312 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_cleaned_seq) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: 'Py_UNICODE* PyUnicode_AsUnicode(PyObject*)' is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4312:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4312 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_cleaned_seq) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4312:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4312 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_cleaned_seq) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function 'bool __pyx_f_5khmer_5_oxli_7parsing_sanitize_sequence(std::string&, std::string&, bool)': khmer/_oxli/parsing.cpp:5733:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5733 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { | ~~~~~~~~~~^~~~~~~~~~~ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from khmer/_oxli/parsing.cpp:4: khmer/_oxli/parsing.cpp: In function 'int __pyx_f_5khmer_5_oxli_7parsing__check_is_pair(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*, __pyx_obj_5khmer_5_oxli_7parsing_Sequence*)': /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11131:49: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 11131 | __pyx_t_1 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: 'Py_UNICODE* PyUnicode_AsUnicode(PyObject*)' is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11131:49: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 11131 | __pyx_t_1 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11131:49: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 11131 | __pyx_t_1 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11304:49: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 11304 | __pyx_t_4 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: 'Py_UNICODE* PyUnicode_AsUnicode(PyObject*)' is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11304:49: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 11304 | __pyx_t_4 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11304:49: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 11304 | __pyx_t_4 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/khmer/_oxli/parsing.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hashing' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c khmer/_oxli/hashing.cpp -o build/temp.linux-x86_64-3.9/khmer/_oxli/hashing.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/khmer/_oxli/hashing.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.graphs' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c khmer/_oxli/graphs.cpp -o build/temp.linux-x86_64-3.9/khmer/_oxli/graphs.o -O3 -std=c++11 -pedantic -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:651: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/graphs.cpp:534: note: this is the location of the previous definition 534 | #define PyInt_Check(op) PyLong_Check(op) | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:651: include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/graphs.cpp:541: note: this is the location of the previous definition 541 | #define PyInt_AsLong PyLong_AsLong | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:651: include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/graphs.cpp:538: note: this is the location of the previous definition 538 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/khmer/_oxli/graphs.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.assembly' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c khmer/_oxli/assembly.cpp -o build/temp.linux-x86_64-3.9/khmer/_oxli/assembly.o -O3 -std=c++11 -pedantic -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:651: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/assembly.cpp:534: note: this is the location of the previous definition 534 | #define PyInt_Check(op) PyLong_Check(op) | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:651: include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/assembly.cpp:541: note: this is the location of the previous definition 541 | #define PyInt_AsLong PyLong_AsLong | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:651: include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/assembly.cpp:538: note: this is the location of the previous definition 538 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/khmer/_oxli/assembly.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so -fopenmp running build_scripts creating build/scripts-3.9 copying and adjusting scripts/extract-paired-reads.py -> build/scripts-3.9 copying and adjusting scripts/unique-kmers.py -> build/scripts-3.9 copying and adjusting scripts/trim-low-abund.py -> build/scripts-3.9 copying and adjusting scripts/split-paired-reads.py -> build/scripts-3.9 copying and adjusting scripts/sample-reads-randomly.py -> build/scripts-3.9 copying and adjusting scripts/readstats.py -> build/scripts-3.9 copying and adjusting scripts/partition-graph.py -> build/scripts-3.9 copying and adjusting scripts/normalize-by-median.py -> build/scripts-3.9 copying and adjusting scripts/merge-partitions.py -> build/scripts-3.9 copying and adjusting scripts/make-initial-stoptags.py -> build/scripts-3.9 copying and adjusting scripts/load-into-counting.py -> build/scripts-3.9 copying and adjusting scripts/load-graph.py -> build/scripts-3.9 copying and adjusting scripts/interleave-reads.py -> build/scripts-3.9 copying and adjusting scripts/find-knots.py -> build/scripts-3.9 copying and adjusting scripts/filter-stoptags.py -> build/scripts-3.9 copying and adjusting scripts/filter-abund.py -> build/scripts-3.9 copying and adjusting scripts/filter-abund-single.py -> build/scripts-3.9 copying and adjusting scripts/fastq-to-fasta.py -> build/scripts-3.9 copying and adjusting scripts/extract-partitions.py -> build/scripts-3.9 copying and adjusting scripts/extract-long-sequences.py -> build/scripts-3.9 copying and adjusting scripts/do-partition.py -> build/scripts-3.9 copying and adjusting scripts/count-median.py -> build/scripts-3.9 copying and adjusting scripts/annotate-partitions.py -> build/scripts-3.9 copying and adjusting scripts/abundance-dist.py -> build/scripts-3.9 copying and adjusting scripts/abundance-dist-single.py -> build/scripts-3.9 changing mode of build/scripts-3.9/extract-paired-reads.py from 644 to 755 changing mode of build/scripts-3.9/unique-kmers.py from 644 to 755 changing mode of build/scripts-3.9/trim-low-abund.py from 644 to 755 changing mode of build/scripts-3.9/split-paired-reads.py from 644 to 755 changing mode of build/scripts-3.9/sample-reads-randomly.py from 644 to 755 changing mode of build/scripts-3.9/readstats.py from 644 to 755 changing mode of build/scripts-3.9/partition-graph.py from 644 to 755 changing mode of build/scripts-3.9/normalize-by-median.py from 644 to 755 changing mode of build/scripts-3.9/merge-partitions.py from 644 to 755 changing mode of build/scripts-3.9/make-initial-stoptags.py from 644 to 755 changing mode of build/scripts-3.9/load-into-counting.py from 644 to 755 changing mode of build/scripts-3.9/load-graph.py from 644 to 755 changing mode of build/scripts-3.9/interleave-reads.py from 644 to 755 changing mode of build/scripts-3.9/find-knots.py from 644 to 755 changing mode of build/scripts-3.9/filter-stoptags.py from 644 to 755 changing mode of build/scripts-3.9/filter-abund.py from 644 to 755 changing mode of build/scripts-3.9/filter-abund-single.py from 644 to 755 changing mode of build/scripts-3.9/fastq-to-fasta.py from 644 to 755 changing mode of build/scripts-3.9/extract-partitions.py from 644 to 755 changing mode of build/scripts-3.9/extract-long-sequences.py from 644 to 755 changing mode of build/scripts-3.9/do-partition.py from 644 to 755 changing mode of build/scripts-3.9/count-median.py from 644 to 755 changing mode of build/scripts-3.9/annotate-partitions.py from 644 to 755 changing mode of build/scripts-3.9/abundance-dist.py from 644 to 755 changing mode of build/scripts-3.9/abundance-dist-single.py from 644 to 755 ln -sf "`pwd`"/.pybuild/pythonX.Y_*/build/khmer/*.so khmer && \ ./setup.py develop --user && ./setup.py build_sphinx running develop running egg_info writing khmer.egg-info/PKG-INFO writing dependency_links to khmer.egg-info/dependency_links.txt writing requirements to khmer.egg-info/requires.txt writing top-level names to khmer.egg-info/top_level.txt reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.hh' under directory 'khmer' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching '*.c' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '[Mm]akefile*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution writing manifest file 'khmer.egg-info/SOURCES.txt' running build_ext skipping 'khmer/_oxli/utils.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/parsing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/hashing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/graphs.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/assembly.cpp' Cython extension (up-to-date) building 'khmer._khmer' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_countgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_counttable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_graphlabels.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashset.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashtable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hllcounter.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_nodegraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_nodetable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_readaligner.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_smallcountgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_smallcounttable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_subsetpartition.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-3.9/src/oxli/assembler.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor 'oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)': include/oxli/assembler.hh:80:23: warning: 'oxli::LinearAssembler::graph' will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ include/oxli/assembler.hh:79:16: warning: 'oxli::WordLength oxli::LinearAssembler::_ksize' [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor 'oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()': src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type 'oxli::LinearAssembler' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38: 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) : | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38: 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 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]': src/oxli/hashtable.cc:512:1: required from here src/oxli/hashtable.cc:103:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 103 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]': src/oxli/hashtable.cc:529:1: required from here src/oxli/hashtable.cc:133:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 133 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hllcounter.cc: In instantiation of 'void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]': src/oxli/hllcounter.cc:524:1: required from here src/oxli/hllcounter.cc:428:40: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 428 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o -O3 -std=c++11 -pedantic -fopenmp In file included from third-party/seqan/core/include/seqan/basic.h:62, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:116, 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, from src/oxli/read_parsers.cc:39: 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, 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, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function 'int seqan::_globalAlignmentScore(const seqan::String&, const seqan::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:74:2: 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, 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, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function 'seqan::Pair > seqan::_alignBandedSmithWatermanTrace(seqan::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:412:2: 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, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: 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 [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/store/store_all.h: In function 'void seqan::convertMatchesToGlobalAlignment(seqan::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:1737:2: 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 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/storage.cc -o build/temp.linux-x86_64-3.9/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/subset.cc -o build/temp.linux-x86_64-3.9/src/oxli/subset.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/subset.cc: In member function 'size_t oxli::SubsetPartition::output_partitioned_file(const string&, const 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 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-3.9/src/oxli/traversal.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:203:31: 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, | ^~~~~~~~~~~~~~~~~~~~~~~ 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 = true; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:203:31: 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 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp creating build/lib.linux-x86_64-3.9 creating build/lib.linux-x86_64-3.9/khmer x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.9/khmer/_khmer.cpython-39-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.utils' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c khmer/_oxli/utils.cpp -o build/temp.linux-x86_64-3.9/khmer/_oxli/utils.o -O3 -std=c++11 -pedantic -fopenmp creating build/lib.linux-x86_64-3.9/khmer/_oxli x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/khmer/_oxli/utils.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.9/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.parsing' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c khmer/_oxli/parsing.cpp -o build/temp.linux-x86_64-3.9/khmer/_oxli/parsing.o -O3 -std=c++11 -pedantic -fopenmp In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from khmer/_oxli/parsing.cpp:4: khmer/_oxli/parsing.cpp: In function 'PyObject* __pyx_pf_5khmer_5_oxli_7parsing_9Alphabets_get(PyObject*)': /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:2339:47: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 2339 | __pyx_t_4 = (__pyx_v_alphabet != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_alphabet) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: 'Py_UNICODE* PyUnicode_AsUnicode(PyObject*)' is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:2339:47: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 2339 | __pyx_t_4 = (__pyx_v_alphabet != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_alphabet) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:2339:47: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 2339 | __pyx_t_4 = (__pyx_v_alphabet != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_alphabet) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function 'PyObject* __pyx_pf_5khmer_5_oxli_7parsing_8Sequence_4name___get__(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*)': /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:3969:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 3969 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_name) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: 'Py_UNICODE* PyUnicode_AsUnicode(PyObject*)' is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:3969:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 3969 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_name) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:3969:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 3969 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_name) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function 'PyObject* __pyx_pf_5khmer_5_oxli_7parsing_8Sequence_8sequence___get__(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*)': /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4057:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4057 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_sequence) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: 'Py_UNICODE* PyUnicode_AsUnicode(PyObject*)' is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4057:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4057 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_sequence) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4057:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4057 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_sequence) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function 'PyObject* __pyx_pf_5khmer_5_oxli_7parsing_8Sequence_11description___get__(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*)': /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4144:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4144 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_description) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: 'Py_UNICODE* PyUnicode_AsUnicode(PyObject*)' is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4144:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4144 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_description) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4144:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4144 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_description) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function 'PyObject* __pyx_pf_5khmer_5_oxli_7parsing_8Sequence_7quality___get__(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*)': /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4228:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4228 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_quality) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: 'Py_UNICODE* PyUnicode_AsUnicode(PyObject*)' is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4228:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4228 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_quality) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4228:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4228 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_quality) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function 'PyObject* __pyx_pf_5khmer_5_oxli_7parsing_8Sequence_11cleaned_seq___get__(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*)': /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4312:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4312 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_cleaned_seq) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: 'Py_UNICODE* PyUnicode_AsUnicode(PyObject*)' is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4312:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4312 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_cleaned_seq) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4312:16: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 4312 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_cleaned_seq) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function 'bool __pyx_f_5khmer_5_oxli_7parsing_sanitize_sequence(std::string&, std::string&, bool)': khmer/_oxli/parsing.cpp:5733:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5733 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { | ~~~~~~~~~~^~~~~~~~~~~ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from khmer/_oxli/parsing.cpp:4: khmer/_oxli/parsing.cpp: In function 'int __pyx_f_5khmer_5_oxli_7parsing__check_is_pair(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*, __pyx_obj_5khmer_5_oxli_7parsing_Sequence*)': /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11131:49: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 11131 | __pyx_t_1 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: 'Py_UNICODE* PyUnicode_AsUnicode(PyObject*)' is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11131:49: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 11131 | __pyx_t_1 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11131:49: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 11131 | __pyx_t_1 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11304:49: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 11304 | __pyx_t_4 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: 'Py_UNICODE* PyUnicode_AsUnicode(PyObject*)' is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11304:49: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 11304 | __pyx_t_4 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: 'Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)' is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro 'PyUnicode_WSTR_LENGTH' 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro 'PyUnicode_GET_SIZE' 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11304:49: note: in expansion of macro '__Pyx_PyUnicode_IS_TRUE' 11304 | __pyx_t_4 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/khmer/_oxli/parsing.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.9/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hashing' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c khmer/_oxli/hashing.cpp -o build/temp.linux-x86_64-3.9/khmer/_oxli/hashing.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/khmer/_oxli/hashing.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.9/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.graphs' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c khmer/_oxli/graphs.cpp -o build/temp.linux-x86_64-3.9/khmer/_oxli/graphs.o -O3 -std=c++11 -pedantic -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:651: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/graphs.cpp:534: note: this is the location of the previous definition 534 | #define PyInt_Check(op) PyLong_Check(op) | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:651: include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/graphs.cpp:541: note: this is the location of the previous definition 541 | #define PyInt_AsLong PyLong_AsLong | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:651: include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/graphs.cpp:538: note: this is the location of the previous definition 538 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/khmer/_oxli/graphs.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.9/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.assembly' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c khmer/_oxli/assembly.cpp -o build/temp.linux-x86_64-3.9/khmer/_oxli/assembly.o -O3 -std=c++11 -pedantic -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:651: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/assembly.cpp:534: note: this is the location of the previous definition 534 | #define PyInt_Check(op) PyLong_Check(op) | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:651: include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/assembly.cpp:541: note: this is the location of the previous definition 541 | #define PyInt_AsLong PyLong_AsLong | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:651: include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/assembly.cpp:538: note: this is the location of the previous definition 538 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/khmer/_oxli/assembly.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.9/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so -fopenmp copying build/lib.linux-x86_64-3.9/khmer/_khmer.cpython-39-x86_64-linux-gnu.so -> khmer copying build/lib.linux-x86_64-3.9/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-3.9/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-3.9/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-3.9/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-3.9/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so -> khmer/_oxli Creating /build/khmer-2.1.2+dfsg/fakehome/.local/lib/python3.9/site-packages/khmer.egg-link (link to .) Adding khmer 2.1.2 to easy-install.pth file Installing extract-paired-reads.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing unique-kmers.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing trim-low-abund.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing split-paired-reads.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing sample-reads-randomly.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing readstats.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing partition-graph.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing normalize-by-median.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing merge-partitions.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing make-initial-stoptags.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing load-into-counting.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing load-graph.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing interleave-reads.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing find-knots.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing filter-stoptags.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing filter-abund.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing filter-abund-single.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing fastq-to-fasta.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing extract-partitions.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing extract-long-sequences.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing do-partition.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing count-median.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing annotate-partitions.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing abundance-dist.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing abundance-dist-single.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installed /build/khmer-2.1.2+dfsg Processing dependencies for khmer==2.1.2 Searching for screed==1.0.5 Best match: screed 1.0.5 Adding screed 1.0.5 to easy-install.pth file Installing screed script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Using /usr/lib/python3/dist-packages Searching for bz2file==0.98 Best match: bz2file 0.98 Adding bz2file 0.98 to easy-install.pth file Using /usr/lib/python3/dist-packages Searching for Cython==0.29.21 Best match: Cython 0.29.21 Adding Cython 0.29.21 to easy-install.pth file Using /usr/lib/python3/dist-packages Finished processing dependencies for khmer==2.1.2 running build_sphinx Running Sphinx v3.4.3 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... 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[100%] user/scripts looking for now-outdated files... none found pickling environment... done checking consistency... /build/khmer-2.1.2+dfsg/doc/dev/hackathon.rst: WARNING: document isn't included in any toctree /build/khmer-2.1.2+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... 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[100%] user/scripts /build/khmer-2.1.2+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: load-into-counting.py -N /build/khmer-2.1.2+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: load-into-counting.py --n_tables /build/khmer-2.1.2+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: load-into-counting.py -x /build/khmer-2.1.2+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: load-into-counting.py --max-tablesize /build/khmer-2.1.2+dfsg/doc/user/scripts.rst:79: WARNING: unknown option: -x /build/khmer-2.1.2+dfsg/doc/user/scripts.rst:79: WARNING: unknown option: -N /build/khmer-2.1.2+dfsg/doc/user/scripts.rst:87: WARNING: unknown option: -x /build/khmer-2.1.2+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 cd src/oxli && /usr/bin/make clean all make[2]: Entering directory '/build/khmer-2.1.2+dfsg/src/oxli' rm -f *.o *.a *.so* oxli.pc g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o hashtable.o hashtable.cc hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]': hashtable.cc:512:1: required from here hashtable.cc:103:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 103 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]': hashtable.cc:529:1: required from here hashtable.cc:133:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 133 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o hashgraph.o hashgraph.cc g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o hllcounter.o hllcounter.cc hllcounter.cc: In instantiation of 'void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]': hllcounter.cc:524:1: required from here hllcounter.cc:428:40: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 428 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o kmer_hash.o kmer_hash.cc g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o labelhash.o labelhash.cc g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-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:203:31: 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 traversal.cc:39: traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]': traversal.cc:203:31: required from here ../../include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ ../../include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o read_aligner.o read_aligner.cc g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o read_parsers.o read_parsers.cc In file included from ../../third-party/seqan/core/include/seqan/basic.h:62, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/align.h:116, 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, from read_parsers.cc:39: ../../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, 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, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function 'int seqan::_globalAlignmentScore(const seqan::String&, const seqan::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:74:2: 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, 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, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function 'seqan::Pair > seqan::_alignBandedSmithWatermanTrace(seqan::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:412:2: 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, from ../../third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from ../../third-party/seqan/core/include/seqan/seq_io.h:83, from read_parsers.cc:39: ../../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 [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/bam_io.h:107, from ../../third-party/seqan/core/include/seqan/store.h:41, from ../../third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from ../../third-party/seqan/core/include/seqan/seq_io.h:83, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/store.h:61, from ../../third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from ../../third-party/seqan/core/include/seqan/seq_io.h:83, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/store/store_all.h: In function 'void seqan::convertMatchesToGlobalAlignment(seqan::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:1737:2: 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 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-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 string&, const string&, bool, oxli::CallbackFn, void*)': subset.cc:136:24: warning: unused variable 'ksize' [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o kmer_filters.o kmer_filters.cc g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-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; | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from assembler.cc:38: ../../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) : | ^~~~~~~~~~~~~~~~~~~~~~ In file included from assembler.cc:38: ../../include/oxli/assembler.hh:153:15: warning: 'oxli::JunctionCountAssembler::traverser' will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ ../../include/oxli/assembler.hh:151:21: warning: 'oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm' [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o alphabets.o alphabets.cc g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -c -o murmur3.o ../../third-party/smhasher/MurmurHash3.cc g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o storage.o storage.cc g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -Wl,-soname=liboxli.so.1 -shared -o liboxli.so.1 hashtable.o hashgraph.o hllcounter.o kmer_hash.o labelhash.o traversal.o read_aligner.o read_parsers.o subset.o kmer_filters.o assembler.o alphabets.o murmur3.o storage.o ln -sf liboxli.so.1 liboxli.so ar rcs liboxli.a hashtable.o hashgraph.o hllcounter.o kmer_hash.o labelhash.o traversal.o read_aligner.o read_parsers.o subset.o kmer_filters.o assembler.o alphabets.o murmur3.o storage.o ranlib liboxli.a sed -e 's,@prefix@,/usr/local,' -e 's,@VERSION@,,' oxli.pc.in >oxli.pc make[2]: Leaving directory '/build/khmer-2.1.2+dfsg/src/oxli' make[1]: Leaving directory '/build/khmer-2.1.2+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-2.1.2+dfsg' dh_auto_install install -d /build/khmer-2.1.2\+dfsg/debian/tmp pybuild --install --test-pytest -i python{version} -p 3.9 --dest-dir /build/khmer-2.1.2\+dfsg/debian/tmp I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/khmer-2.1.2+dfsg/debian/khmer '--install-scripts=/usr/lib/khmer/bin' running install running build running build_py running egg_info writing khmer.egg-info/PKG-INFO writing dependency_links to khmer.egg-info/dependency_links.txt writing requirements to khmer.egg-info/requires.txt writing top-level names to khmer.egg-info/top_level.txt reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.hh' under directory 'khmer' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching '*.c' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '[Mm]akefile*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution writing manifest file 'khmer.egg-info/SOURCES.txt' copying khmer/_oxli/assembly.cpp -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.cpp -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.cpp -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.cpp -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/utils.cpp -> /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli UPDATING /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_version.py set /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_version.py to '2.1.2' running build_ext skipping 'khmer/_oxli/utils.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/parsing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/hashing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/graphs.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/assembly.cpp' Cython extension (up-to-date) building 'khmer._khmer' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_countgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_counttable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_graphlabels.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashset.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashtable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hllcounter.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_nodegraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_nodetable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_readaligner.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_smallcountgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_smallcounttable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_subsetpartition.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-3.9/src/oxli/assembler.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor 'oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)': include/oxli/assembler.hh:80:23: warning: 'oxli::LinearAssembler::graph' will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ include/oxli/assembler.hh:79:16: warning: 'oxli::WordLength oxli::LinearAssembler::_ksize' [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor 'oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()': src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type 'oxli::LinearAssembler' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38: 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) : | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38: 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 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]': src/oxli/hashtable.cc:512:1: required from here src/oxli/hashtable.cc:103:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 103 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]': src/oxli/hashtable.cc:529:1: required from here src/oxli/hashtable.cc:133:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 133 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hllcounter.cc: In instantiation of 'void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]': src/oxli/hllcounter.cc:524:1: required from here src/oxli/hllcounter.cc:428:40: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 428 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o -O3 -std=c++11 -pedantic -fopenmp In file included from third-party/seqan/core/include/seqan/basic.h:62, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:116, 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, from src/oxli/read_parsers.cc:39: 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, 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, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function 'int seqan::_globalAlignmentScore(const seqan::String&, const seqan::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:74:2: 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, 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, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function 'seqan::Pair > seqan::_alignBandedSmithWatermanTrace(seqan::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:412:2: 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, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: 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 [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/store/store_all.h: In function 'void seqan::convertMatchesToGlobalAlignment(seqan::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:1737:2: 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 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/storage.cc -o build/temp.linux-x86_64-3.9/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/subset.cc -o build/temp.linux-x86_64-3.9/src/oxli/subset.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/subset.cc: In member function 'size_t oxli::SubsetPartition::output_partitioned_file(const string&, const 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 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-3.9/src/oxli/traversal.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:203:31: 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, | ^~~~~~~~~~~~~~~~~~~~~~~ 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 = true; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:203:31: 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 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_khmer.cpython-39-x86_64-linux-gnu.so -fopenmp running build_scripts running install_lib creating /build/khmer-2.1.2+dfsg/debian/khmer creating /build/khmer-2.1.2+dfsg/debian/khmer/usr creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9 creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli/__init__.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli/build_graph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli/functions.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli/partition.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_khmer.cpython-39-x86_64-linux-gnu.so -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_version.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.cpp -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.cpp -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.cpp -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.cpp -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.cpp -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.pyx -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/traversal.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.pyx -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/oxli_types.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hllcounter.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.pyx -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.pyx -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.pyx -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/__init__.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/valid-read-testing.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/unclean-reads.fastq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/truncated.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-transcript.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-sweep-reads.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-sweep-reads.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-sweep-contigs.fp -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-short.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-reads.fq.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-reads.fq.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-reads.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-overlap2.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-overlap1.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-output-partitions.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-multi.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-large.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-labels.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-graph5.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-graph2.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-graph.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-filter-abund-Ns.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-fastq-reads.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-fastq-reads.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-fastq-n-reads.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-error-reads.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-empty.fa.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-empty.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-paired.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-paired.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-impaired.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-3.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.paired2.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.paired.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/single-read.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/single-read.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/simple-genome.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/simple-genome-reads.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/real-partition-tiny.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/real-partition-small.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/readaligner-k12.json -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/readaligner-default.json -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-31-c.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-b.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.odd.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fq.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fq.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fa.part -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fa.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fa.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.even.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-X2.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired_one.base.dif.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.malformat.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.malformat.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fq.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fa.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fa.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-slash1.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-slash1.fq.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-slash1.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fq.se -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fq.pe -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fa.se -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fa.pe -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed-witherror.fa.pe -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed-broken.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed-2.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken4.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken4.fq.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken3.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken3.fq.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken2.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken2.fq.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.paired_bad -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.badright -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.badleft -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/old-style-format-w-comments.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/normC20k20.ct -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/multi-output.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/goodversion-k32.tagset -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/goodversion-k32.stoptags -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/goodversion-k12.ht.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/goodversion-k12.ht -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/filter-test-B.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/filter-test-A.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/fakelump.fa.stoptags.txt -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/fakelump.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/empty-file.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/empty-file.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/empty-file -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/dn-test-some-paired-all-keep.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/dn-test-none-paired.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/dn-test-all-paired-all-keep.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/combine_parts_1.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/casava_18-pe.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/bogus.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/biglump-random-20-a.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/banding-reads.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/badversion-k32.tagset -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/badversion-k32.stoptags -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/badversion-k12.ht -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/badversion-k12.ct -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/all-A.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/README.rst -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/100-reads.fq.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/100-reads.fq.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/.gitignore -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__init__.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/graph_features.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_banding.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_countgraph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_counting_single.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_counttable.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_cpython_hierarchy.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_cython_assembly.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_cython_parsing.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_filter_abund.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_functions.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_graph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_hashset.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_hll.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_labelhash.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_lump.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_nibblestorage.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_nodegraph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_normalize_by_median.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_oxli_functions.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_read_aligner.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_read_handling.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_sandbox_scripts.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_script_arguments.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_script_output.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_scripts.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_sequence_validation.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_streaming_io.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_subset_graph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_tabletype.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_threaded_sequence_processor.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_version.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_read_parsers.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/khmer_tst_utils.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/__init__.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/kfile.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/khmer_args.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/khmer_logger.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/thread_utils.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/trimming.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/utils.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli/__init__.py to __init__.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli/build_graph.py to build_graph.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli/functions.py to functions.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli/partition.py to partition.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_version.py to _version.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli/__init__.py to __init__.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__init__.py to __init__.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/graph_features.py to graph_features.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_banding.py to test_banding.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_countgraph.py to test_countgraph.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_counting_single.py to test_counting_single.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_counttable.py to test_counttable.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_cpython_hierarchy.py to test_cpython_hierarchy.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_cython_assembly.py to test_cython_assembly.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_cython_parsing.py to test_cython_parsing.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_filter_abund.py to test_filter_abund.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_functions.py to test_functions.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_graph.py to test_graph.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_hashset.py to test_hashset.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_hll.py to test_hll.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_labelhash.py to test_labelhash.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_lump.py to test_lump.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_nibblestorage.py to test_nibblestorage.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_nodegraph.py to test_nodegraph.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_normalize_by_median.py to test_normalize_by_median.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_oxli_functions.py to test_oxli_functions.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_read_aligner.py to test_read_aligner.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_read_handling.py to test_read_handling.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_sandbox_scripts.py to test_sandbox_scripts.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_script_arguments.py to test_script_arguments.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_script_output.py to test_script_output.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_scripts.py to test_scripts.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_sequence_validation.py to test_sequence_validation.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_streaming_io.py to test_streaming_io.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py to test_subset_graph.cpython-39.pyc /usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py:61: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py:82: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py:278: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py:476: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py:509: SyntaxWarning: "is" with a literal. Did you mean "=="? byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_tabletype.py to test_tabletype.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_threaded_sequence_processor.py to test_threaded_sequence_processor.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_version.py to test_version.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_read_parsers.py to test_read_parsers.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/khmer_tst_utils.py to khmer_tst_utils.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/__init__.py to __init__.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/kfile.py to kfile.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/khmer_args.py to khmer_args.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/khmer_logger.py to khmer_logger.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/thread_utils.py to thread_utils.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/trimming.py to trimming.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/utils.py to utils.cpython-39.pyc running install_egg_info Copying khmer.egg-info to /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer-2.1.2.egg-info Skipping SOURCES.txt running install_scripts creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/abundance-dist-single.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/abundance-dist.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/annotate-partitions.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/count-median.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/do-partition.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/extract-long-sequences.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/extract-partitions.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/fastq-to-fasta.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/filter-abund-single.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/filter-abund.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/filter-stoptags.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/find-knots.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/interleave-reads.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/load-graph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/load-into-counting.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/make-initial-stoptags.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/merge-partitions.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/normalize-by-median.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/partition-graph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/readstats.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/sample-reads-randomly.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/split-paired-reads.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/trim-low-abund.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/unique-kmers.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/extract-paired-reads.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/abundance-dist-single.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/abundance-dist.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/annotate-partitions.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/count-median.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/do-partition.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/extract-long-sequences.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/extract-partitions.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/fastq-to-fasta.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/filter-abund-single.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/filter-abund.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/filter-stoptags.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/find-knots.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/interleave-reads.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/load-graph.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/load-into-counting.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/make-initial-stoptags.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/merge-partitions.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/normalize-by-median.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/partition-graph.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/readstats.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/sample-reads-randomly.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/split-paired-reads.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/trim-low-abund.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/unique-kmers.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/extract-paired-reads.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 3.9 I: pybuild base:232: cd /build/khmer-2.1.2+dfsg; export PATH=/build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path ; cd /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build; export PYTHONPATH=/build/khmer-2.1.2+dfsg; python3.9 -m pytest -m 'not known_failing and not jenkins and not huge and not noroot' -q ============================= test session starts ============================== platform linux -- Python 3.9.2, pytest-6.0.2, py-1.10.0, pluggy-0.13.0 rootdir: /build/khmer-2.1.2+dfsg, configfile: pytest.ini collected 2732 items / 52 deselected / 2680 selected khmer/tests/test_banding.py ............ [ 0%] khmer/tests/test_countgraph.py ......................................... [ 1%] .................................................. [ 3%] khmer/tests/test_counting_single.py ......................... [ 4%] khmer/tests/test_counttable.py .......... [ 5%] khmer/tests/test_cpython_hierarchy.py .... [ 5%] khmer/tests/test_cython_assembly.py .................................... [ 6%] ........................................................................ [ 9%] ........................................................................ [ 12%] ........................................................................ [ 14%] ........................................................................ [ 17%] ......... [ 17%] khmer/tests/test_cython_parsing.py ..................................... [ 19%] .... [ 19%] khmer/tests/test_filter_abund.py ................... [ 19%] khmer/tests/test_functions.py .................. [ 20%] khmer/tests/test_graph.py ............................ [ 21%] khmer/tests/test_hashset.py ............. [ 22%] khmer/tests/test_hll.py ...................... [ 22%] khmer/tests/test_labelhash.py ................. [ 23%] khmer/tests/test_lump.py ...... [ 23%] khmer/tests/test_nibblestorage.py ..... [ 24%] khmer/tests/test_nodegraph.py .......................................... [ 25%] ........................ [ 26%] khmer/tests/test_normalize_by_median.py ................................ [ 27%] ...... [ 27%] khmer/tests/test_oxli_functions.py .... [ 28%] khmer/tests/test_read_aligner.py ..................x. [ 28%] khmer/tests/test_read_handling.py ................................ [ 30%] khmer/tests/test_read_parsers.py .............................. [ 31%] khmer/tests/test_sandbox_scripts.py sssssssssss [ 31%] khmer/tests/test_script_arguments.py ............................ [ 32%] khmer/tests/test_script_output.py ........... [ 32%] khmer/tests/test_scripts.py ............................................ [ 34%] ........................................................................ [ 37%] .............................. [ 38%] khmer/tests/test_sequence_validation.py ................................ [ 39%] ............ [ 40%] khmer/tests/test_streaming_io.py ............................ [ 41%] khmer/tests/test_subset_graph.py ........................... [ 42%] khmer/tests/test_tabletype.py .....................................s.s.s [ 43%] ........................................................................ [ 46%] ........................................................................ [ 49%] .................. [ 49%] khmer/tests/test_threaded_sequence_processor.py ...... [ 49%] khmer/tests/test_version.py . [ 50%] tests/test_banding.py ............ [ 50%] tests/test_countgraph.py ............................................... [ 52%] ............................................ [ 53%] tests/test_counting_single.py ......................... [ 54%] tests/test_counttable.py .......... [ 55%] tests/test_cpython_hierarchy.py .... [ 55%] tests/test_cython_assembly.py .......................................... [ 56%] ........................................................................ [ 59%] ........................................................................ [ 62%] ........................................................................ [ 64%] ........................................................................ [ 67%] ... [ 67%] tests/test_cython_parsing.py ......................................... [ 69%] tests/test_filter_abund.py ................... [ 69%] tests/test_functions.py .................. [ 70%] tests/test_graph.py ............................ [ 71%] tests/test_hashset.py ............. [ 72%] tests/test_hll.py ...................... [ 72%] tests/test_labelhash.py ................. [ 73%] tests/test_lump.py ...... [ 73%] tests/test_nibblestorage.py ..... [ 74%] tests/test_nodegraph.py ................................................ [ 75%] .................. [ 76%] tests/test_normalize_by_median.py ...................................... [ 77%] [ 77%] tests/test_oxli_functions.py .... [ 78%] tests/test_read_aligner.py ..................x. [ 78%] tests/test_read_handling.py ................................ [ 80%] tests/test_read_parsers.py .............................. [ 81%] tests/test_sandbox_scripts.py sssssssssss [ 81%] tests/test_script_arguments.py ............................ [ 82%] tests/test_script_output.py ........... [ 82%] tests/test_scripts.py .................................................. [ 84%] ........................................................................ [ 87%] ........................ [ 88%] tests/test_sequence_validation.py ...................................... [ 89%] ...... [ 90%] tests/test_streaming_io.py ............................ [ 91%] tests/test_subset_graph.py ........................... [ 92%] tests/test_tabletype.py .....................................s.s.s...... [ 93%] ........................................................................ [ 96%] ........................................................................ [ 99%] ............ [ 99%] tests/test_threaded_sequence_processor.py ...... [ 99%] tests/test_version.py . [100%] ==== 2650 passed, 28 skipped, 52 deselected, 2 xfailed in 132.90s (0:02:12) ==== rm -fr -- /tmp/dh-xdg-rundir-2DZrpKZH make[1]: Leaving directory '/build/khmer-2.1.2+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 -d /build/khmer-2.1.2\+dfsg/debian/tmp pybuild --install --test-pytest -i python{version} -p 3.9 --dest-dir /build/khmer-2.1.2\+dfsg/debian/tmp I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/khmer-2.1.2+dfsg/debian/khmer '--install-scripts=/usr/lib/khmer/bin' running install running build running build_py running egg_info writing khmer.egg-info/PKG-INFO writing dependency_links to khmer.egg-info/dependency_links.txt writing requirements to khmer.egg-info/requires.txt writing top-level names to khmer.egg-info/top_level.txt reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.hh' under directory 'khmer' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching '*.c' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '[Mm]akefile*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution writing manifest file 'khmer.egg-info/SOURCES.txt' UPDATING /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_version.py set /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_version.py to '2.1.2' running build_ext skipping 'khmer/_oxli/utils.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/parsing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/hashing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/graphs.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/assembly.cpp' Cython extension (up-to-date) building 'khmer._khmer' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_countgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_counttable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_graphlabels.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashset.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashtable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hllcounter.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_nodegraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_nodetable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_readaligner.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_smallcountgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_smallcounttable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_subsetpartition.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-3.9/src/oxli/assembler.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor 'oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)': include/oxli/assembler.hh:80:23: warning: 'oxli::LinearAssembler::graph' will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ include/oxli/assembler.hh:79:16: warning: 'oxli::WordLength oxli::LinearAssembler::_ksize' [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor 'oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()': src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type 'oxli::LinearAssembler' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38: 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) : | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38: 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 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]': src/oxli/hashtable.cc:512:1: required from here src/oxli/hashtable.cc:103:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 103 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]': src/oxli/hashtable.cc:529:1: required from here src/oxli/hashtable.cc:133:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 133 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hllcounter.cc: In instantiation of 'void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]': src/oxli/hllcounter.cc:524:1: required from here src/oxli/hllcounter.cc:428:40: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 428 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o -O3 -std=c++11 -pedantic -fopenmp In file included from third-party/seqan/core/include/seqan/basic.h:62, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:116, 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, from src/oxli/read_parsers.cc:39: 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, 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, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function 'int seqan::_globalAlignmentScore(const seqan::String&, const seqan::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:74:2: 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, 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, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function 'seqan::Pair > seqan::_alignBandedSmithWatermanTrace(seqan::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:412:2: 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, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: 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 [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/store/store_all.h: In function 'void seqan::convertMatchesToGlobalAlignment(seqan::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:1737:2: 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 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/storage.cc -o build/temp.linux-x86_64-3.9/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/subset.cc -o build/temp.linux-x86_64-3.9/src/oxli/subset.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/subset.cc: In member function 'size_t oxli::SubsetPartition::output_partitioned_file(const string&, const 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 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-3.9/src/oxli/traversal.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:203:31: 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, | ^~~~~~~~~~~~~~~~~~~~~~~ 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 = true; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:203:31: 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 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_khmer.cpython-39-x86_64-linux-gnu.so -fopenmp running build_scripts running install_lib creating /build/khmer-2.1.2+dfsg/debian/khmer creating /build/khmer-2.1.2+dfsg/debian/khmer/usr creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9 creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli/__pycache__/partition.cpython-39.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli/__pycache__/functions.cpython-39.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli/__pycache__/build_graph.cpython-39.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli/__pycache__/__init__.cpython-39.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli/__init__.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli/build_graph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli/functions.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli/partition.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_khmer.cpython-39-x86_64-linux-gnu.so -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_version.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/__pycache__/trimming.cpython-39.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/__pycache__/thread_utils.cpython-39.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/__pycache__/kfile.cpython-39.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/__pycache__/khmer_logger.cpython-39.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/__pycache__/utils.cpython-39.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/__pycache__/khmer_args.cpython-39.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/__pycache__/_version.cpython-39.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/__pycache__/__init__.cpython-39.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/__pycache__ creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/__pycache__/__init__.cpython-39.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.cpp -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.cpp -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.cpp -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.cpp -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.cpp -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.pyx -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/traversal.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.pyx -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/oxli_types.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hllcounter.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.pyx -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.pyx -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.pyx -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/__init__.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_version.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_threaded_sequence_processor.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_tabletype.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_subset_graph.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_streaming_io.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_sequence_validation.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_script_output.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_script_arguments.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_sandbox_scripts.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_read_parsers.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_read_handling.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_read_aligner.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_oxli_functions.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_normalize_by_median.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_nodegraph.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_nibblestorage.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_lump.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_labelhash.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_hll.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_hashset.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_graph.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_functions.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_scripts.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_filter_abund.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_cython_parsing.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/graph_features.cpython-39.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_cython_assembly.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_cpython_hierarchy.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_counttable.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_counting_single.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_countgraph.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/khmer_tst_utils.cpython-39.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/test_banding.cpython-39-pytest-6.0.2.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__pycache__/__init__.cpython-39.pyc -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__pycache__ creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/valid-read-testing.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/unclean-reads.fastq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/truncated.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-transcript.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-sweep-reads.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-sweep-reads.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-sweep-contigs.fp -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-short.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-reads.fq.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-reads.fq.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-reads.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-overlap2.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-overlap1.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-output-partitions.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-multi.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-large.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-labels.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-graph5.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-graph2.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-graph.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-filter-abund-Ns.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-fastq-reads.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-fastq-reads.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-fastq-n-reads.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-error-reads.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-empty.fa.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-empty.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-paired.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-paired.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-impaired.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-3.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.paired2.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.paired.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/single-read.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/single-read.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/simple-genome.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/simple-genome-reads.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/real-partition-tiny.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/real-partition-small.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/readaligner-k12.json -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/readaligner-default.json -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-31-c.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-b.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.odd.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fq.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fq.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fa.part -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fa.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fa.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.even.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-X2.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired_one.base.dif.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.malformat.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.malformat.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fq.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fa.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fa.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-slash1.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-slash1.fq.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-slash1.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fq.se -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fq.pe -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fa.se -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fa.pe -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed-witherror.fa.pe -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed-broken.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed-2.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken4.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken4.fq.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken3.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken3.fq.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken2.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken2.fq.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.paired_bad -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.badright -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.badleft -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/old-style-format-w-comments.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/normC20k20.ct -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/multi-output.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/goodversion-k32.tagset -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/goodversion-k32.stoptags -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/goodversion-k12.ht.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/goodversion-k12.ht -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/filter-test-B.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/filter-test-A.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/fakelump.fa.stoptags.txt -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/fakelump.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/empty-file.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/empty-file.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/empty-file -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/dn-test-some-paired-all-keep.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/dn-test-none-paired.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/dn-test-all-paired-all-keep.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/combine_parts_1.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/casava_18-pe.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/bogus.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/biglump-random-20-a.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/banding-reads.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/badversion-k32.tagset -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/badversion-k32.stoptags -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/badversion-k12.ht -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/badversion-k12.ct -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/all-A.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/README.rst -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/100-reads.fq.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/100-reads.fq.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/.gitignore -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__init__.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/graph_features.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_banding.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_countgraph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_counting_single.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_counttable.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_cpython_hierarchy.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_cython_assembly.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_cython_parsing.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_filter_abund.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_functions.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_graph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_hashset.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_hll.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_labelhash.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_lump.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_nibblestorage.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_nodegraph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_normalize_by_median.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_oxli_functions.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_read_aligner.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_read_handling.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_sandbox_scripts.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_script_arguments.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_script_output.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_scripts.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_sequence_validation.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_streaming_io.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_subset_graph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_tabletype.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_threaded_sequence_processor.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_version.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_read_parsers.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/khmer_tst_utils.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/__init__.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/kfile.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/khmer_args.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/khmer_logger.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/thread_utils.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/trimming.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/utils.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli/__init__.py to __init__.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli/build_graph.py to build_graph.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli/functions.py to functions.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli/partition.py to partition.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_version.py to _version.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli/__init__.py to __init__.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__init__.py to __init__.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/graph_features.py to graph_features.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_banding.py to test_banding.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_countgraph.py to test_countgraph.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_counting_single.py to test_counting_single.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_counttable.py to test_counttable.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_cpython_hierarchy.py to test_cpython_hierarchy.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_cython_assembly.py to test_cython_assembly.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_cython_parsing.py to test_cython_parsing.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_filter_abund.py to test_filter_abund.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_functions.py to test_functions.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_graph.py to test_graph.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_hashset.py to test_hashset.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_hll.py to test_hll.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_labelhash.py to test_labelhash.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_lump.py to test_lump.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_nibblestorage.py to test_nibblestorage.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_nodegraph.py to test_nodegraph.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_normalize_by_median.py to test_normalize_by_median.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_oxli_functions.py to test_oxli_functions.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_read_aligner.py to test_read_aligner.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_read_handling.py to test_read_handling.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_sandbox_scripts.py to test_sandbox_scripts.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_script_arguments.py to test_script_arguments.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_script_output.py to test_script_output.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_scripts.py to test_scripts.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_sequence_validation.py to test_sequence_validation.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_streaming_io.py to test_streaming_io.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py to test_subset_graph.cpython-39.pyc /usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py:61: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py:82: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py:278: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py:476: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py:509: SyntaxWarning: "is" with a literal. Did you mean "=="? byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_tabletype.py to test_tabletype.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_threaded_sequence_processor.py to test_threaded_sequence_processor.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_version.py to test_version.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_read_parsers.py to test_read_parsers.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/khmer_tst_utils.py to khmer_tst_utils.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/__init__.py to __init__.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/kfile.py to kfile.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/khmer_args.py to khmer_args.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/khmer_logger.py to khmer_logger.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/thread_utils.py to thread_utils.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/trimming.py to trimming.cpython-39.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/utils.py to utils.cpython-39.pyc running install_egg_info Copying khmer.egg-info to /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer-2.1.2.egg-info Skipping SOURCES.txt running install_scripts creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/abundance-dist-single.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/abundance-dist.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/annotate-partitions.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/count-median.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/do-partition.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/extract-long-sequences.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/extract-partitions.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/fastq-to-fasta.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/filter-abund-single.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/filter-abund.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/filter-stoptags.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/find-knots.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/interleave-reads.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/load-graph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/load-into-counting.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/make-initial-stoptags.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/merge-partitions.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/normalize-by-median.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/partition-graph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/readstats.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/sample-reads-randomly.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/split-paired-reads.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/trim-low-abund.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/unique-kmers.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/extract-paired-reads.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/abundance-dist-single.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/abundance-dist.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/annotate-partitions.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/count-median.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/do-partition.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/extract-long-sequences.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/extract-partitions.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/fastq-to-fasta.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/filter-abund-single.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/filter-abund.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/filter-stoptags.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/find-knots.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/interleave-reads.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/load-graph.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/load-into-counting.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/make-initial-stoptags.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/merge-partitions.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/normalize-by-median.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/partition-graph.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/readstats.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/sample-reads-randomly.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/split-paired-reads.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/trim-low-abund.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/unique-kmers.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/extract-paired-reads.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-2.1.2+dfsg' cd src/oxli && /usr/bin/make PREFIX=../debian/tmp install make[2]: Entering directory '/build/khmer-2.1.2+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-2.1.2+dfsg/src/oxli' dh_install install -d debian/khmer-common/usr/share/file/khmer cp --reflink=auto -a ./include/oxli/magic debian/khmer-common/usr/share/file/khmer/ install -d debian/.debhelper/generated/khmer-common install -d debian/khmer//usr/share/metainfo/ cp --reflink=auto -a ./debian/khmer.metainfo.xml debian/khmer//usr/share/metainfo// install -d debian/khmer/usr/bin/ cp --reflink=auto -a ./debian/bin/khmer debian/khmer/usr/bin// install -d debian/.debhelper/generated/khmer install -d debian/liboxli1/usr/lib/x86_64-linux-gnu cp --reflink=auto -a ./src/oxli/liboxli.so.1 debian/liboxli1/usr/lib/x86_64-linux-gnu/ install -d debian/.debhelper/generated/liboxli1 install -d debian/liboxli-dev/usr/include/oxli cp --reflink=auto -a ./include/oxli/alphabets.hh ./include/oxli/assembler.hh ./include/oxli/hashgraph.hh ./include/oxli/hashtable.hh ./include/oxli/hllcounter.hh ./include/oxli/kmer_filters.hh ./include/oxli/kmer_hash.hh ./include/oxli/labelhash.hh ./include/oxli/oxli.hh ./include/oxli/oxli_exception.hh ./include/oxli/read_aligner.hh ./include/oxli/read_parsers.hh ./include/oxli/storage.hh ./include/oxli/subset.hh ./include/oxli/traversal.hh debian/liboxli-dev/usr/include/oxli/ install -d debian/liboxli-dev/usr/include/oxli/smhasher cp --reflink=auto -a ./third-party/smhasher/MurmurHash3.h debian/liboxli-dev/usr/include/oxli/smhasher/ install -d debian/liboxli-dev/usr/lib/x86_64-linux-gnu cp --reflink=auto -a ./src/oxli/liboxli.a ./src/oxli/liboxli.so debian/liboxli-dev/usr/lib/x86_64-linux-gnu/ install -d debian/liboxli-dev/usr/lib/x86_64-linux-gnu/pkgconfig cp --reflink=auto -a ./src/oxli/oxli.pc debian/liboxli-dev/usr/lib/x86_64-linux-gnu/pkgconfig/ install -d debian/.debhelper/generated/liboxli-dev find debian/khmer -name .gitignore -delete make[1]: Leaving directory '/build/khmer-2.1.2+dfsg' dh_installdocs -O--buildsystem=pybuild install -d debian/khmer-common/usr/share/doc/khmer-common cd './build/sphinx/html/..' && find 'html' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/khmer-2.1.2+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 -d debian/khmer-common/usr/share/doc-base/ install -p -m0644 debian/doc-base debian/khmer-common/usr/share/doc-base/khmer install -d debian/khmer/usr/share/doc/khmer install -p -m0644 debian/copyright debian/khmer/usr/share/doc/khmer/copyright install -d debian/liboxli1/usr/share/doc/liboxli1 install -p -m0644 debian/copyright debian/liboxli1/usr/share/doc/liboxli1/copyright install -d debian/liboxli-dev/usr/share/doc/liboxli-dev install -p -m0644 debian/copyright debian/liboxli-dev/usr/share/doc/liboxli-dev/copyright rm -f debian/khmer-common.debhelper.log debian/khmer.debhelper.log debian/liboxli-dev.debhelper.log debian/liboxli1.debhelper.log debian/rules override_dh_sphinxdoc make[1]: Entering directory '/build/khmer-2.1.2+dfsg' dh_sphinxdoc ln -sf ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js ln -sf ../../../../javascript/sphinxdoc/1.0/language_data.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js 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/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/doctools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js ln -sf ../../../../javascript/sphinxdoc/1.0/jquery.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/.buildinfo (grep -a -s -v sphinxdoc:Depends debian/khmer-common.substvars; echo "sphinxdoc:Depends=libjs-sphinxdoc (>= 2.0)") > debian/khmer-common.substvars.new mv debian/khmer-common.substvars.new debian/khmer-common.substvars (grep -a -s -v sphinxdoc:Depends debian/khmer-common.substvars; echo "sphinxdoc:Depends=libjs-sphinxdoc (>= 1.8), libjs-sphinxdoc (>= 2.0)") > debian/khmer-common.substvars.new mv debian/khmer-common.substvars.new debian/khmer-common.substvars (grep -a -s -v sphinxdoc:Depends debian/khmer-common.substvars; echo "sphinxdoc:Depends=libjs-sphinxdoc (>= 1.0), libjs-sphinxdoc (>= 1.8), libjs-sphinxdoc (>= 2.0)") > debian/khmer-common.substvars.new mv debian/khmer-common.substvars.new debian/khmer-common.substvars (grep -a -s -v sphinxdoc:Depends debian/khmer-common.substvars; echo "sphinxdoc:Depends=libjs-sphinxdoc (>= 1.0), libjs-sphinxdoc (>= 1.8), libjs-sphinxdoc (>= 2.0), libjs-sphinxdoc (>= 2.4.3-5~)") > debian/khmer-common.substvars.new mv debian/khmer-common.substvars.new debian/khmer-common.substvars (grep -a -s -v sphinxdoc:Built-Using debian/khmer-common.substvars; echo "sphinxdoc:Built-Using=sphinx (= 3.4.3-2)") > debian/khmer-common.substvars.new 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 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/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/_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/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/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 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/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/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 , 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/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/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 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/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/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 , 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/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/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 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/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/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 , 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", 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/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/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 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/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/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 , 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/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/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 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/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/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 , 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/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/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 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/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/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 , 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/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/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 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/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/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 , 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/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/_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 11783387 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-2.1.2+dfsg' dh_installchangelogs -O--buildsystem=pybuild install -p -m0644 debian/changelog debian/liboxli1/usr/share/doc/liboxli1/changelog.Debian install -p -m0644 ./CHANGELOG.md debian/liboxli1/usr/share/doc/liboxli1/changelog install -p -m0644 debian/changelog 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 -p -m0644 debian/changelog debian/khmer-common/usr/share/doc/khmer-common/changelog.Debian install -p -m0644 ./CHANGELOG.md debian/khmer-common/usr/share/doc/khmer-common/changelog install -p -m0644 debian/changelog debian/khmer/usr/share/doc/khmer/changelog.Debian install -p -m0644 ./CHANGELOG.md debian/khmer/usr/share/doc/khmer/changelog dh_installman -O--buildsystem=pybuild install -d debian/khmer/usr/share/man/man1/ install -p -m0644 ./debian/khmer.1 debian/khmer/usr/share/man/man1/khmer.1 man-recode --to-code UTF-8 --suffix .dh-new debian/khmer/usr/share/man/man1/khmer.1 mv debian/khmer/usr/share/man/man1/khmer.1.dh-new debian/khmer/usr/share/man/man1/khmer.1 chmod 0644 -- debian/khmer/usr/share/man/man1/khmer.1 dh_python3 -O--buildsystem=pybuild D: dh_python3 dh_python3:161: version: 4.20201102+nmu1 D: dh_python3 dh_python3:162: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:163: options: {'guess_deps': True, 'skip_private': False, 'verbose': False, 'arch': None, 'package': None, 'no_package': None, 'compile_all': False, 'vrange': None, 'regexpr': None, 'accept_upstream_versions': False, 'depends': None, 'depends_section': None, 'recommends': None, 'recommends_section': None, 'suggests': None, 'suggests_section': None, 'requires': None, 'shebang': None, 'ignore_shebangs': False, 'clean_dbg_pkg': True, 'no_ext_rename': False, 'no_shebang_rewrite': False, 'O': '--buildsystem=pybuild'} D: dh_python3 dh_python3:164: args: [] D: dh_python3 dh_python3:165: supported Python versions: 3.9 (default=3.9) D: dh_python3 debhelper:99: skipping package khmer-common (missing ${python3:Depends} in Depends) D: dh_python3 debhelper:99: skipping package liboxli1 (missing ${python3:Depends} in Depends) D: dh_python3 debhelper:99: skipping package liboxli-dev (missing ${python3:Depends} in Depends) D: dh_python3 debhelper:152: source=khmer, binary packages=['khmer'] D: dh_python3 dh_python3:183: processing package khmer... D: dh_python3 fs:49: moving files from debian/khmer/usr/lib/python3.9/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:260: package khmer details = {'requires.txt': {'debian/khmer/usr/lib/python3/dist-packages/khmer-2.1.2.egg-info/requires.txt'}, 'egg-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('3.9')}, 'ext_no_version': set()} D: dh_python3 depends:117: generating dependencies for package khmer D: dh_python3 pydist:142: trying to find dependency for Cython>=0.25.2 (python=None) D: dh_python3 pydist:142: trying to find dependency for bz2file (python=None) D: dh_python3 pydist:142: trying to find dependency for screed>=1.0 (python=None) D: dh_python3 depends:275: D={'python3 (<< 3.10)', 'python3-screed (>= 1.0)', 'python3:any', 'python3 (>= 3.9~)', 'python3-bz2file', 'cython3 (>= 0.26.1)'}; R=[]; S=[]; E=[], B=[]; RT=[('/usr/lib/khmer', '')] dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild install -d debian/khmer/usr/share/lintian/overrides install -p -m0644 debian/khmer.lintian-overrides debian/khmer/usr/share/lintian/overrides/khmer install -d debian/liboxli1/usr/share/lintian/overrides install -p -m0644 debian/liboxli1.lintian-overrides debian/liboxli1/usr/share/lintian/overrides/liboxli1 dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt ln -s ../../CITATION debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/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 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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 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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 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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/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/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/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/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/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/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 1609766292 as canonical time 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/minus.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 1609766292 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/empty-file.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/random-20-a.fa.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.truncated.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 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/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 gzip -9nf usr/share/doc/liboxli1/changelog usr/share/doc/liboxli1/changelog.Debian cd '/build/khmer-2.1.2+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-2.1.2+dfsg' cd '/build/khmer-2.1.2+dfsg' cd '/build/khmer-2.1.2+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/khmer-common ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/khmer ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/liboxli1 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/liboxli-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/liboxli1/usr/share/doc -type f -a -true -a ! -regex 'debian/liboxli1/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/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/liboxli-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/liboxli-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/khmer-common/usr/share/doc -type f -a -true -a ! -regex 'debian/khmer-common/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli1/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/khmer/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/liboxli1/usr/share/lintian/overrides -type f -a -true -a -true -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-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/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli1 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/khmer -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/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/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/liboxli-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/khmer/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/liboxli-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/khmer/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild install -d debian/khmer/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/khmer/usr/lib/debug/.dwz/x86_64-linux-gnu/khmer.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/khmer.debug -- debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-39-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so objcopy --compress-debug-sections debian/khmer/usr/lib/debug/.dwz/x86_64-linux-gnu/khmer.debug dwz -- debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 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 -d debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/39 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/39/32d09eb3f99b65e643407f58b90216945b855b.debug install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/83 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-39-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/83/110460faa62284464ade475afcdfaa4e1aafd0.debug chmod 0644 -- debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/39/32d09eb3f99b65e643407f58b90216945b855b.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/39/32d09eb3f99b65e643407f58b90216945b855b.debug debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 install -d debian/.debhelper/liboxli1/dbgsym-root/usr/share/doc ln -s liboxli1 debian/.debhelper/liboxli1/dbgsym-root/usr/share/doc/liboxli1-dbgsym chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/83/110460faa62284464ade475afcdfaa4e1aafd0.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-39-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/83/110460faa62284464ade475afcdfaa4e1aafd0.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-39-x86_64-linux-gnu.so install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/3d objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/3d/7de51b05c9382fa1c5c5e3968e6e22e581cbf1.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/3d/7de51b05c9382fa1c5c5e3968e6e22e581cbf1.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/3d/7de51b05c9382fa1c5c5e3968e6e22e581cbf1.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/c8 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/c8/6ce5247b29c2b62429e818653578d1ac78fa0e.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/c8/6ce5247b29c2b62429e818653578d1ac78fa0e.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/c8/6ce5247b29c2b62429e818653578d1ac78fa0e.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/f8 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/f8/4d76d6a0c480ff4e2cd7296f3d48066622eeb2.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/f8/4d76d6a0c480ff4e2cd7296f3d48066622eeb2.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/f8/4d76d6a0c480ff4e2cd7296f3d48066622eeb2.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/55 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/55/dd8453aafa37f404eb325c387e3119411584b8.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/55/dd8453aafa37f404eb325c387e3119411584b8.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/55/dd8453aafa37f404eb325c387e3119411584b8.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/23 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/23/8aa536b8bebe104876c3e8aef4e262955bd900.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/23/8aa536b8bebe104876c3e8aef4e262955bd900.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/23/8aa536b8bebe104876c3e8aef4e262955bd900.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/khmer/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/khmer/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/khmer/usr/lib/debug install -d debian/.debhelper/khmer/dbgsym-root/usr/share/doc ln -s khmer debian/.debhelper/khmer/dbgsym-root/usr/share/doc/khmer-dbgsym dh_makeshlibs -a -O--buildsystem=pybuild rm -f debian/khmer/DEBIAN/shlibs rm -f debian/liboxli1/DEBIAN/shlibs install -d debian/liboxli1/DEBIAN echo "liboxli 1 liboxli1 (>= 2.1.2+dfsg)" >> debian/liboxli1/DEBIAN/shlibs chmod 0644 -- debian/liboxli1/DEBIAN/shlibs mv debian/.debhelper/generated/liboxli1/triggers.new debian/.debhelper/generated/liboxli1/triggers rm -f debian/liboxli-dev/DEBIAN/shlibs dh_shlibdeps -a -O--buildsystem=pybuild dpkg-shlibdeps -Tdebian/liboxli1.substvars debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 install -d debian/khmer/DEBIAN dpkg-shlibdeps -Tdebian/khmer.substvars debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-39-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so dpkg-shlibdeps: warning: symbol gztell64 used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol BZ2_bzRead used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol 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 gzread 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 gzeof 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 crc32 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 inflateInit2_ used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: 13 other similar warnings have been skipped (use -v to see them all) dh_installdeb -O--buildsystem=pybuild install -d debian/khmer-common/DEBIAN cp -f debian/khmer-common.postinst debian/khmer-common/DEBIAN/postinst [META] Replace #TOKEN#s in "debian/khmer-common/DEBIAN/postinst" chmod 0755 -- debian/khmer-common/DEBIAN/postinst cp -f debian/khmer-common.postrm debian/khmer-common/DEBIAN/postrm [META] Replace #TOKEN#s in "debian/khmer-common/DEBIAN/postrm" chmod 0755 -- debian/khmer-common/DEBIAN/postrm printf '#!/bin/sh\nset -e\n' > debian/khmer/DEBIAN/postinst cat debian/khmer.postinst.debhelper >> debian/khmer/DEBIAN/postinst chmod 0755 -- debian/khmer/DEBIAN/postinst printf '#!/bin/sh\nset -e\n' > debian/khmer/DEBIAN/prerm cat debian/khmer.prerm.debhelper >> debian/khmer/DEBIAN/prerm chmod 0755 -- debian/khmer/DEBIAN/prerm install -p -m0644 debian/.debhelper/generated/liboxli1/triggers debian/liboxli1/DEBIAN/triggers install -d debian/liboxli-dev/DEBIAN dh_gencontrol -O--buildsystem=pybuild echo misc:Depends= >> debian/khmer-common.substvars echo misc:Pre-Depends= >> debian/khmer-common.substvars dpkg-gencontrol -pkhmer-common -ldebian/changelog -Tdebian/khmer-common.substvars -Pdebian/khmer-common echo misc:Depends= >> debian/liboxli-dev.substvars echo misc:Pre-Depends= >> debian/liboxli-dev.substvars dpkg-gencontrol -pliboxli-dev -ldebian/changelog -Tdebian/liboxli-dev.substvars -Pdebian/liboxli-dev echo misc:Depends= >> debian/khmer.substvars echo misc:Pre-Depends= >> debian/khmer.substvars install -d debian/.debhelper/khmer/dbgsym-root/DEBIAN dpkg-gencontrol -pkhmer -ldebian/changelog -Tdebian/khmer.substvars -Pdebian/.debhelper/khmer/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=khmer-dbgsym "-DDepends=khmer (= \${binary:Version})" "-DDescription=debug symbols for khmer" "-DBuild-Ids=238aa536b8bebe104876c3e8aef4e262955bd900 3d7de51b05c9382fa1c5c5e3968e6e22e581cbf1 55dd8453aafa37f404eb325c387e3119411584b8 83110460faa62284464ade475afcdfaa4e1aafd0 c86ce5247b29c2b62429e818653578d1ac78fa0e f84d76d6a0c480ff4e2cd7296f3d48066622eeb2" -DSection=debug -UMulti-Arch -UReplaces -UBreaks echo misc:Depends= >> debian/liboxli1.substvars echo misc:Pre-Depends= >> debian/liboxli1.substvars install -d debian/.debhelper/liboxli1/dbgsym-root/DEBIAN dpkg-gencontrol -pliboxli1 -ldebian/changelog -Tdebian/liboxli1.substvars -Pdebian/.debhelper/liboxli1/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=liboxli1-dbgsym "-DDepends=liboxli1 (= \${binary:Version})" "-DDescription=debug symbols for liboxli1" -DBuild-Ids=3932d09eb3f99b65e643407f58b90216945b855b -DSection=debug -UReplaces -UBreaks chmod 0644 -- debian/liboxli-dev/DEBIAN/control dpkg-gencontrol: warning: package khmer: substitution variable ${python3:Versions} unused, but is defined 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/.debhelper/liboxli1/dbgsym-root/DEBIAN/control dpkg-gencontrol -pliboxli1 -ldebian/changelog -Tdebian/liboxli1.substvars -Pdebian/liboxli1 dpkg-gencontrol: warning: package khmer: substitution variable ${python3:Versions} unused, but is defined chmod 0644 -- debian/khmer/DEBIAN/control chmod 0644 -- debian/liboxli1/DEBIAN/control dh_md5sums -O--buildsystem=pybuild cd debian/khmer-common >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/liboxli1 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/liboxli-dev >/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 chmod 0644 -- debian/liboxli1/DEBIAN/md5sums 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 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/khmer .. dpkg-deb --root-owner-group --build debian/.debhelper/khmer/dbgsym-root .. dpkg-deb --root-owner-group --build debian/.debhelper/liboxli1/dbgsym-root .. dpkg-deb --root-owner-group --build debian/liboxli1 .. dpkg-deb --root-owner-group --build debian/liboxli-dev .. dpkg-deb: building package 'khmer-common' in '../khmer-common_2.1.2+dfsg-8_all.deb'. dpkg-deb: building package 'khmer-dbgsym' in '../khmer-dbgsym_2.1.2+dfsg-8_amd64.deb'. dpkg-deb: building package 'liboxli1-dbgsym' in '../liboxli1-dbgsym_2.1.2+dfsg-8_amd64.deb'. dpkg-deb: building package 'khmer' in '../khmer_2.1.2+dfsg-8_amd64.deb'. dpkg-deb: building package 'liboxli1' in '../liboxli1_2.1.2+dfsg-8_amd64.deb'. dpkg-deb: building package 'liboxli-dev' in '../liboxli-dev_2.1.2+dfsg-8_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../khmer_2.1.2+dfsg-8_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/147165/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/147165/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/147165 and its subdirectories I: Current time: Wed Sep 4 12:05:47 +14 2024 I: pbuilder-time-stamp: 1725401147