Sun Jul 18 00:27:40 UTC 2021 I: starting to build khmer/bullseye/arm64 on jenkins on '2021-07-18 00:27' Sun Jul 18 00:27:40 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_20/20643/console.log Sun Jul 18 00:27:40 UTC 2021 I: Downloading source for bullseye/khmer=2.1.2+dfsg-8 --2021-07-18 00:27:40-- http://cdn-fastly.deb.debian.org/debian/pool/main/k/khmer/khmer_2.1.2+dfsg-8.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2679 (2.6K) Saving to: ‘khmer_2.1.2+dfsg-8.dsc’ 0K .. 100% 140M=0s 2021-07-18 00:27:40 (140 MB/s) - ‘khmer_2.1.2+dfsg-8.dsc’ saved [2679/2679] Sun Jul 18 00:27:40 UTC 2021 I: khmer_2.1.2+dfsg-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: khmer Binary: khmer-common, khmer, liboxli1, liboxli-dev Architecture: any-arm64 any-ia64 any-sparc64 all amd64 Version: 2.1.2+dfsg-8 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Kevin Murray Homepage: https://khmer.readthedocs.org Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/khmer Vcs-Git: https://salsa.debian.org/med-team/khmer.git Testsuite: autopkgtest Testsuite-Triggers: build-essential, libbz2-dev, pkg-config, python3-pytest, python3-pytest-runner, zlib1g-dev Build-Depends: debhelper-compat (= 13), dh-python, dh-exec, python3-guzzle-sphinx-theme, python3, python3-dev, python3-all-dev, python3-setuptools, python3-screed (>= 1.0), python3-pytest, python3-pytest-runner, python3-sphinx, python3-sphinxcontrib.autoprogram, cython3 (>= 0.26.1), zlib1g-dev, libbz2-dev, asciidoctor, rdfind Package-List: khmer deb science optional arch=amd64,any-arm64,any-ia64,any-sparc64 khmer-common deb science optional arch=all liboxli-dev deb libdevel optional arch=amd64,any-arm64,any-ia64,any-sparc64 liboxli1 deb libs optional arch=amd64,any-arm64,any-ia64,any-sparc64 Checksums-Sha1: 414c7e2516edb37b8e712c12ed1075a6f081d0c7 18086617 khmer_2.1.2+dfsg.orig.tar.gz 2a77d3844c3ce2c9322396c91dd25beb2d79faa0 14148 khmer_2.1.2+dfsg-8.debian.tar.xz Checksums-Sha256: 7b6e01d4af574e83ccf74ea3b11b2c6ed89a4af8d01b1154d93074a0a16045c2 18086617 khmer_2.1.2+dfsg.orig.tar.gz 355ba2dead9eec520ac7e74ed91f249728d8e2cd001c99fa4870c0b6924835fd 14148 khmer_2.1.2+dfsg-8.debian.tar.xz Files: 9cfe54c467302b3232a553494d62dbb0 18086617 khmer_2.1.2+dfsg.orig.tar.gz 251147b97c7b4020d463fdb6d978a858 14148 khmer_2.1.2+dfsg-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAl/zGXUACgkQPCZ2P2xn 5uLZkxAAundCGf1VLNHDjMO7s3qj3HPI/iEmZnGGLwSt/7Zyge6T6DPlSHAxavZi B6FMIWn2TLIfOAizvX24XTmxE12Sewu1Lb7y98QovSXvmM0Kv3swaMjRnuF6LHav ReHJ8zeWw3N2lJku6Ombu2WzEt4vcGkkuZnajaRdHxeBu32oVfDcmMkjrW6Jh8Aa h1A+lWYJvTSxQpknhx2AY/VPMiy1RGHI9u4NO+pN3RhkEywQitC/XDmjVMrhxmsM atfEywOsIpdxL7GLlVZypmMmV3j2WE4MzDmtZQPJ3M+SFWsm8xw50GmiiYKu5qvF zMlX+u8OI17pOpy7545RXLzwmKDtXxZT9hGdrn+J/sna0lHMONabN6f9OLX62j7s L65bU4csYqPdmAbu+Di6Z6p+K/m5Iy8/qLNMZbBqc2aTKzHyPq4aCrC3KwBPsLs3 /vGXHPwpBaJv52YzwwK0cLJPCebldXhe2ZDWb0cohXFlo01EctUN32sBmQ46AUM0 1H67miXw0zy2pjysAxFCXtStAB2Xjg/4O4DPlCGNAupWcaTyNi+O2qvn0WFZIeyO m4OPR+MCGg5coiLgBJyfADdlR5Yn2iM9LPA+6m42y7PAJBhQPIhWCI5gdRRsl+Kt 5QG6bUbXkfRj1qOWEXgACGat2qusBzMvAiujYS65+GPQnoh/y3Y= =KK3d -----END PGP SIGNATURE----- Sun Jul 18 00:27:40 UTC 2021 I: Checking whether the package is not for us Sun Jul 18 00:27:40 UTC 2021 I: Starting 1st build on remote node codethink13-arm64.debian.net. Sun Jul 18 00:27:40 UTC 2021 I: Preparing to do remote build '1' on codethink13-arm64.debian.net. Sun Jul 18 00:49:55 UTC 2021 I: Deleting $TMPDIR on codethink13-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Aug 19 18:50:45 -12 2022 I: pbuilder-time-stamp: 1660978245 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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.fvlKT8F9/trustedkeys.kbx': General error gpgv: Signature made Mon Jan 4 01:34:45 2021 -12 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/21872/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='21872' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.uvpcoPqUCG/pbuilderrc_Uoi2 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.uvpcoPqUCG/b1 --logfile b1/build.log khmer_2.1.2+dfsg-8.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink13-arm64 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 21 2021 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 Feb 7 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 7 2021 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 93744 Mar 2 2021 gzip -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 161960 Feb 7 2021 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Feb 7 2021 more -rwsr-xr-x 1 root root 51360 Feb 7 2021 mount -rwxr-xr-x 1 root root 14496 Feb 7 2021 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 2021 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 19 03:48 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Feb 7 2021 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 7 2021 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 7 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/21872/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: arm64 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 ... 19646 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 50.6 MB of archives. After unpacking 205 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-minimal arm64 3.9.2-1 [797 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libmpdec3 arm64 2.5.1-1 [84.4 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 python3.9 arm64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 sgml-base all 1.30 [15.1 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 openssl arm64 1.1.1k-1 [829 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 ca-certificates all 20210119 [158 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 rubygems-integration all 1.18 [6704 B] Get: 27 http://deb.debian.org/debian bullseye/main arm64 rake all 13.0.3-1 [84.7 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 ruby-minitest all 5.13.0-1 [57.3 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 ruby-power-assert all 1.1.7-2 [11.5 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 ruby-test-unit all 3.3.9-1 [86.1 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 libmd0 arm64 1.0.3-3 [27.9 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libbsd0 arm64 0.11.3-1 [106 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 libedit2 arm64 3.1-20191231-2+b1 [92.1 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libyaml-0-2 arm64 0.2.2-1 [45.1 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 libruby2.7 arm64 2.7.3-2 [4026 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 ruby2.7 arm64 2.7.3-2 [744 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 ruby-rubygems all 3.2.5-2 [281 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 ruby arm64 1:2.7+2 [11.7 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 ruby-asciidoctor all 2.0.12-2 [206 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 asciidoctor all 2.0.12-2 [83.9 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 cython3 arm64 0.29.21-3+b1 [1239 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 59 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 60 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 61 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 62 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 63 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 64 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 65 http://deb.debian.org/debian bullseye/main arm64 dh-exec arm64 0.23.2 [26.2 kB] Get: 66 http://deb.debian.org/debian bullseye/main arm64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 67 http://deb.debian.org/debian bullseye/main arm64 python3-distutils all 3.9.2-1 [143 kB] Get: 68 http://deb.debian.org/debian bullseye/main arm64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 69 http://deb.debian.org/debian bullseye/main arm64 xml-core all 0.18+nmu1 [23.8 kB] Get: 70 http://deb.debian.org/debian bullseye/main arm64 docutils-common all 0.16+dfsg-4 [129 kB] Get: 71 http://deb.debian.org/debian bullseye/main arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-2 [164 kB] Get: 72 http://deb.debian.org/debian bullseye/main arm64 fonts-liberation all 1:1.07.4-11 [828 kB] Get: 73 http://deb.debian.org/debian bullseye/main arm64 libbz2-dev arm64 1.0.8-4 [31.5 kB] Get: 74 http://deb.debian.org/debian bullseye/main arm64 libexpat1-dev arm64 2.2.10-2 [126 kB] Get: 75 http://deb.debian.org/debian bullseye/main arm64 libjs-bootstrap all 3.4.1+dfsg-2 [173 kB] Get: 76 http://deb.debian.org/debian bullseye/main arm64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 77 http://deb.debian.org/debian bullseye/main arm64 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 78 http://deb.debian.org/debian bullseye/main arm64 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 79 http://deb.debian.org/debian bullseye/main arm64 libpython3.9 arm64 3.9.2-1 [1556 kB] Get: 80 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-dev arm64 3.9.2-1 [3835 kB] Get: 81 http://deb.debian.org/debian bullseye/main arm64 libpython3-dev arm64 3.9.2-3 [21.7 kB] Get: 82 http://deb.debian.org/debian bullseye/main arm64 libpython3-all-dev arm64 3.9.2-3 [1068 B] Get: 83 http://deb.debian.org/debian bullseye/main arm64 python-babel-localedata all 2.8.0+dfsg.1-7 [4997 kB] Get: 84 http://deb.debian.org/debian bullseye/main arm64 python3-alabaster all 0.7.8-1.1 [18.6 kB] Get: 85 http://deb.debian.org/debian bullseye/main arm64 python3-all arm64 3.9.2-3 [1056 B] Get: 86 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get: 87 http://deb.debian.org/debian bullseye/main arm64 python3.9-dev arm64 3.9.2-1 [515 kB] Get: 88 http://deb.debian.org/debian bullseye/main arm64 python3-dev arm64 3.9.2-3 [24.8 kB] Get: 89 http://deb.debian.org/debian bullseye/main arm64 python3-all-dev arm64 3.9.2-3 [1064 B] Get: 90 http://deb.debian.org/debian bullseye/main arm64 python3-attr all 20.3.0-1 [52.9 kB] Get: 91 http://deb.debian.org/debian bullseye/main arm64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 92 http://deb.debian.org/debian bullseye/main arm64 python3-tz all 2021.1-1 [34.8 kB] Get: 93 http://deb.debian.org/debian bullseye/main arm64 python3-babel all 2.8.0+dfsg.1-7 [100 kB] Get: 94 http://deb.debian.org/debian bullseye/main arm64 python3-bz2file all 0.98-3 [8012 B] Get: 95 http://deb.debian.org/debian bullseye/main arm64 python3-certifi all 2020.6.20-1 [151 kB] Get: 96 http://deb.debian.org/debian bullseye/main arm64 python3-chardet all 4.0.0-1 [99.0 kB] Get: 97 http://deb.debian.org/debian bullseye/main arm64 python3-roman all 2.0.0-5 [9064 B] Get: 98 http://deb.debian.org/debian bullseye/main arm64 python3-docutils all 0.16+dfsg-4 [384 kB] Get: 99 http://deb.debian.org/debian bullseye/main arm64 sphinx-common all 3.4.3-2 [578 kB] Get: 100 http://deb.debian.org/debian bullseye/main arm64 python3-imagesize all 1.2.0-2 [5824 B] Get: 101 http://deb.debian.org/debian bullseye/main arm64 python3-markupsafe arm64 1.1.1-1+b3 [15.2 kB] Get: 102 http://deb.debian.org/debian bullseye/main arm64 python3-jinja2 all 2.11.3-1 [114 kB] Get: 103 http://deb.debian.org/debian bullseye/main arm64 python3-pyparsing all 2.4.7-1 [109 kB] Get: 104 http://deb.debian.org/debian bullseye/main arm64 python3-packaging all 20.9-2 [33.5 kB] Get: 105 http://deb.debian.org/debian bullseye/main arm64 python3-pygments all 2.7.1+dfsg-2.1 [657 kB] Get: 106 http://deb.debian.org/debian bullseye/main arm64 python3-idna all 2.10-1 [37.4 kB] Get: 107 http://deb.debian.org/debian bullseye/main arm64 python3-six all 1.16.0-1 [17.1 kB] Get: 108 http://deb.debian.org/debian bullseye/main arm64 python3-urllib3 all 1.26.5-1~exp1 [114 kB] Get: 109 http://deb.debian.org/debian bullseye/main arm64 python3-requests all 2.25.1+dfsg-2 [69.3 kB] Get: 110 http://deb.debian.org/debian bullseye/main arm64 python3-snowballstemmer all 2.1.0-1 [58.7 kB] Get: 111 http://deb.debian.org/debian bullseye/main arm64 python3-sphinx all 3.4.3-2 [545 kB] Get: 112 http://deb.debian.org/debian bullseye/main arm64 python3-guzzle-sphinx-theme all 0.7.11-5 [1346 kB] Get: 113 http://deb.debian.org/debian bullseye/main arm64 python3-more-itertools all 4.2.0-3 [42.7 kB] Get: 114 http://deb.debian.org/debian bullseye/main arm64 python3-zipp all 1.0.0-3 [6060 B] Get: 115 http://deb.debian.org/debian bullseye/main arm64 python3-importlib-metadata all 1.6.0-2 [10.3 kB] Get: 116 http://deb.debian.org/debian bullseye/main arm64 python3-iniconfig all 1.1.1-1 [6308 B] Get: 117 http://deb.debian.org/debian bullseye/main arm64 python3-pluggy all 0.13.0-6 [22.3 kB] Get: 118 http://deb.debian.org/debian bullseye/main arm64 python3-py all 1.10.0-1 [94.2 kB] Get: 119 http://deb.debian.org/debian bullseye/main arm64 python3-toml all 0.10.1-1 [15.9 kB] Get: 120 http://deb.debian.org/debian bullseye/main arm64 python3-pytest all 6.0.2-2 [211 kB] Get: 121 http://deb.debian.org/debian bullseye/main arm64 python3-setuptools all 52.0.0-4 [366 kB] Get: 122 http://deb.debian.org/debian bullseye/main arm64 python3-pytest-runner all 2.11.1-1.2 [8528 B] Get: 123 http://deb.debian.org/debian bullseye/main arm64 python3-screed all 1.0.5-1 [109 kB] Get: 124 http://deb.debian.org/debian bullseye/main arm64 python3-sphinxcontrib.autoprogram all 0.1.5-2 [9692 B] Get: 125 http://deb.debian.org/debian bullseye/main arm64 rdfind arm64 1.4.1-1+b2 [38.7 kB] Fetched 50.6 MB in 2s (31.3 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 ... 19646 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../3-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:arm64. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_arm64.deb ... Unpacking libpython3.9-minimal:arm64 (3.9.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../6-libexpat1_2.2.10-2_arm64.deb ... Unpacking libexpat1:arm64 (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_arm64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:arm64 (3.9.2-1) ... Setting up libexpat1:arm64 (2.2.10-2) ... 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 ... 20513 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_arm64.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:arm64. Preparing to unpack .../2-libmpdec3_2.5.1-1_arm64.deb ... Unpacking libmpdec3:arm64 (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:arm64. Preparing to unpack .../4-libreadline8_8.1-1_arm64.deb ... Unpacking libreadline8:arm64 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:arm64. Preparing to unpack .../5-libpython3.9-stdlib_3.9.2-1_arm64.deb ... Unpacking libpython3.9-stdlib:arm64 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../6-python3.9_3.9.2-1_arm64.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../7-libpython3-stdlib_3.9.2-3_arm64.deb ... Unpacking libpython3-stdlib:arm64 (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 ... 20934 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_arm64.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) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_1.1.1k-1_arm64.deb ... Unpacking openssl (1.1.1k-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../006-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.21-4_arm64.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. Preparing to unpack .../014-ruby-test-unit_3.3.9-1_all.deb ... Unpacking ruby-test-unit (3.3.9-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../015-ruby-xmlrpc_0.3.0-2_all.deb ... Unpacking ruby-xmlrpc (0.3.0-2) ... Selecting previously unselected package libmd0:arm64. Preparing to unpack .../016-libmd0_1.0.3-3_arm64.deb ... Unpacking libmd0:arm64 (1.0.3-3) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../017-libbsd0_0.11.3-1_arm64.deb ... Unpacking libbsd0:arm64 (0.11.3-1) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../018-libedit2_3.1-20191231-2+b1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20191231-2+b1) ... Selecting previously unselected package libyaml-0-2:arm64. Preparing to unpack .../019-libyaml-0-2_0.2.2-1_arm64.deb ... Unpacking libyaml-0-2:arm64 (0.2.2-1) ... Selecting previously unselected package libruby2.7:arm64. Preparing to unpack .../020-libruby2.7_2.7.3-2_arm64.deb ... Unpacking libruby2.7:arm64 (2.7.3-2) ... Selecting previously unselected package ruby2.7. Preparing to unpack .../021-ruby2.7_2.7.3-2_arm64.deb ... Unpacking ruby2.7 (2.7.3-2) ... 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_arm64.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:arm64. Preparing to unpack .../026-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../027-m4_1.4.18-5_arm64.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_arm64.deb ... Unpacking cython3 (0.29.21-3+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../033-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. 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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:arm64 (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+b2) ... Setting up libmagic1:arm64 (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:arm64 (2.2.10-2) ... Setting up ruby-test-unit (3.3.9-1) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libsigsegv2:arm64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Setting up libmd0:arm64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up fonts-liberation (1:1.07.4-11) ... Setting up libmpdec3:arm64 (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 (1.1.1k-1) ... Setting up libbsd0:arm64 (0.11.3-1) ... Setting up libelf1:arm64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7) ... Setting up libjs-bootstrap (3.4.1+dfsg-2) ... Setting up libjs-underscore (1.9.1~dfsg-3) ... Setting up libbz2-dev:arm64 (1.0.8-4) ... Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libedit2:arm64 (3.1-20191231-2+b1) ... Setting up libreadline8:arm64 (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 (1.11.0-1) ... 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:arm64 (3.9.2-1) ... Setting up libpython3-stdlib:arm64 (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:arm64 (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:arm64 (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 (1.16.0-1) ... 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:arm64 (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:arm64 (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 (2.7.3-2) ... 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:arm64 (2.7.3-2) ... Processing triggers for libc-bin (2.31-12) ... 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: Running cd /build/khmer-2.1.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-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 arm64 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-arm64' 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-arm64-3.9 creating build/temp.linux-arm64-3.9/src creating build/temp.linux-arm64-3.9/src/khmer creating build/temp.linux-arm64-3.9/src/oxli creating build/temp.linux-arm64-3.9/third-party creating build/temp.linux-arm64-3.9/third-party/smhasher aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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) : | ^~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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) { | ^~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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) { | ^~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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()); | ^~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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(); | ^~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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, | ^~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp aarch64-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-arm64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-arm64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-arm64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-arm64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-arm64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-arm64-3.9/src/khmer/_cpy_utils.o build/temp.linux-arm64-3.9/src/oxli/alphabets.o build/temp.linux-arm64-3.9/src/oxli/assembler.o build/temp.linux-arm64-3.9/src/oxli/hashgraph.o build/temp.linux-arm64-3.9/src/oxli/hashtable.o build/temp.linux-arm64-3.9/src/oxli/hllcounter.o build/temp.linux-arm64-3.9/src/oxli/kmer_filters.o build/temp.linux-arm64-3.9/src/oxli/kmer_hash.o build/temp.linux-arm64-3.9/src/oxli/labelhash.o build/temp.linux-arm64-3.9/src/oxli/read_aligner.o build/temp.linux-arm64-3.9/src/oxli/read_parsers.o build/temp.linux-arm64-3.9/src/oxli/storage.o build/temp.linux-arm64-3.9/src/oxli/subset.o build/temp.linux-arm64-3.9/src/oxli/traversal.o build/temp.linux-arm64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_khmer.cpython-39-aarch64-linux-gnu.so -fopenmp building 'khmer._oxli.utils' extension creating build/temp.linux-arm64-3.9/khmer creating build/temp.linux-arm64-3.9/khmer/_oxli aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/khmer/_oxli/utils.o -O3 -std=c++11 -pedantic -fopenmp aarch64-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-arm64-3.9/khmer/_oxli/utils.o build/temp.linux-arm64-3.9/src/khmer/_cpy_utils.o build/temp.linux-arm64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-arm64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-arm64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-arm64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-arm64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-arm64-3.9/src/oxli/read_parsers.o build/temp.linux-arm64-3.9/src/oxli/kmer_hash.o build/temp.linux-arm64-3.9/src/oxli/hashtable.o build/temp.linux-arm64-3.9/src/oxli/hashgraph.o build/temp.linux-arm64-3.9/src/oxli/labelhash.o build/temp.linux-arm64-3.9/src/oxli/subset.o build/temp.linux-arm64-3.9/src/oxli/read_aligner.o build/temp.linux-arm64-3.9/src/oxli/hllcounter.o build/temp.linux-arm64-3.9/src/oxli/traversal.o build/temp.linux-arm64-3.9/src/oxli/kmer_filters.o build/temp.linux-arm64-3.9/src/oxli/assembler.o build/temp.linux-arm64-3.9/src/oxli/alphabets.o build/temp.linux-arm64-3.9/src/oxli/storage.o build/temp.linux-arm64-3.9/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-aarch64-linux-gnu.so -fopenmp building 'khmer._oxli.parsing' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-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-arm64-3.9/khmer/_oxli/parsing.o build/temp.linux-arm64-3.9/src/khmer/_cpy_utils.o build/temp.linux-arm64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-arm64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-arm64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-arm64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-arm64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-arm64-3.9/src/oxli/read_parsers.o build/temp.linux-arm64-3.9/src/oxli/kmer_hash.o build/temp.linux-arm64-3.9/src/oxli/hashtable.o build/temp.linux-arm64-3.9/src/oxli/hashgraph.o build/temp.linux-arm64-3.9/src/oxli/labelhash.o build/temp.linux-arm64-3.9/src/oxli/subset.o build/temp.linux-arm64-3.9/src/oxli/read_aligner.o build/temp.linux-arm64-3.9/src/oxli/hllcounter.o build/temp.linux-arm64-3.9/src/oxli/traversal.o build/temp.linux-arm64-3.9/src/oxli/kmer_filters.o build/temp.linux-arm64-3.9/src/oxli/assembler.o build/temp.linux-arm64-3.9/src/oxli/alphabets.o build/temp.linux-arm64-3.9/src/oxli/storage.o build/temp.linux-arm64-3.9/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-aarch64-linux-gnu.so -fopenmp building 'khmer._oxli.hashing' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/khmer/_oxli/hashing.o -O3 -std=c++11 -pedantic -fopenmp aarch64-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-arm64-3.9/khmer/_oxli/hashing.o build/temp.linux-arm64-3.9/src/khmer/_cpy_utils.o build/temp.linux-arm64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-arm64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-arm64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-arm64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-arm64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-arm64-3.9/src/oxli/read_parsers.o build/temp.linux-arm64-3.9/src/oxli/kmer_hash.o build/temp.linux-arm64-3.9/src/oxli/hashtable.o build/temp.linux-arm64-3.9/src/oxli/hashgraph.o build/temp.linux-arm64-3.9/src/oxli/labelhash.o build/temp.linux-arm64-3.9/src/oxli/subset.o build/temp.linux-arm64-3.9/src/oxli/read_aligner.o build/temp.linux-arm64-3.9/src/oxli/hllcounter.o build/temp.linux-arm64-3.9/src/oxli/traversal.o build/temp.linux-arm64-3.9/src/oxli/kmer_filters.o build/temp.linux-arm64-3.9/src/oxli/assembler.o build/temp.linux-arm64-3.9/src/oxli/alphabets.o build/temp.linux-arm64-3.9/src/oxli/storage.o build/temp.linux-arm64-3.9/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-aarch64-linux-gnu.so -fopenmp building 'khmer._oxli.graphs' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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 | aarch64-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-arm64-3.9/khmer/_oxli/graphs.o build/temp.linux-arm64-3.9/src/khmer/_cpy_utils.o build/temp.linux-arm64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-arm64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-arm64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-arm64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-arm64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-arm64-3.9/src/oxli/read_parsers.o build/temp.linux-arm64-3.9/src/oxli/kmer_hash.o build/temp.linux-arm64-3.9/src/oxli/hashtable.o build/temp.linux-arm64-3.9/src/oxli/hashgraph.o build/temp.linux-arm64-3.9/src/oxli/labelhash.o build/temp.linux-arm64-3.9/src/oxli/subset.o build/temp.linux-arm64-3.9/src/oxli/read_aligner.o build/temp.linux-arm64-3.9/src/oxli/hllcounter.o build/temp.linux-arm64-3.9/src/oxli/traversal.o build/temp.linux-arm64-3.9/src/oxli/kmer_filters.o build/temp.linux-arm64-3.9/src/oxli/assembler.o build/temp.linux-arm64-3.9/src/oxli/alphabets.o build/temp.linux-arm64-3.9/src/oxli/storage.o build/temp.linux-arm64-3.9/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-aarch64-linux-gnu.so -fopenmp building 'khmer._oxli.assembly' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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 | aarch64-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-arm64-3.9/khmer/_oxli/assembly.o build/temp.linux-arm64-3.9/src/khmer/_cpy_utils.o build/temp.linux-arm64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-arm64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-arm64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-arm64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-arm64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-arm64-3.9/src/oxli/read_parsers.o build/temp.linux-arm64-3.9/src/oxli/kmer_hash.o build/temp.linux-arm64-3.9/src/oxli/hashtable.o build/temp.linux-arm64-3.9/src/oxli/hashgraph.o build/temp.linux-arm64-3.9/src/oxli/labelhash.o build/temp.linux-arm64-3.9/src/oxli/subset.o build/temp.linux-arm64-3.9/src/oxli/read_aligner.o build/temp.linux-arm64-3.9/src/oxli/hllcounter.o build/temp.linux-arm64-3.9/src/oxli/traversal.o build/temp.linux-arm64-3.9/src/oxli/kmer_filters.o build/temp.linux-arm64-3.9/src/oxli/assembler.o build/temp.linux-arm64-3.9/src/oxli/alphabets.o build/temp.linux-arm64-3.9/src/oxli/storage.o build/temp.linux-arm64-3.9/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-aarch64-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 creating build/temp.linux-aarch64-3.9 creating build/temp.linux-aarch64-3.9/src creating build/temp.linux-aarch64-3.9/src/khmer creating build/temp.linux-aarch64-3.9/src/oxli creating build/temp.linux-aarch64-3.9/third-party creating build/temp.linux-aarch64-3.9/third-party/smhasher aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/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) : | ^~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/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) { | ^~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/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) { | ^~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/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()); | ^~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/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(); | ^~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/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, | ^~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp creating build/lib.linux-aarch64-3.9 creating build/lib.linux-aarch64-3.9/khmer aarch64-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-aarch64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_utils.o build/temp.linux-aarch64-3.9/src/oxli/alphabets.o build/temp.linux-aarch64-3.9/src/oxli/assembler.o build/temp.linux-aarch64-3.9/src/oxli/hashgraph.o build/temp.linux-aarch64-3.9/src/oxli/hashtable.o build/temp.linux-aarch64-3.9/src/oxli/hllcounter.o build/temp.linux-aarch64-3.9/src/oxli/kmer_filters.o build/temp.linux-aarch64-3.9/src/oxli/kmer_hash.o build/temp.linux-aarch64-3.9/src/oxli/labelhash.o build/temp.linux-aarch64-3.9/src/oxli/read_aligner.o build/temp.linux-aarch64-3.9/src/oxli/read_parsers.o build/temp.linux-aarch64-3.9/src/oxli/storage.o build/temp.linux-aarch64-3.9/src/oxli/subset.o build/temp.linux-aarch64-3.9/src/oxli/traversal.o build/temp.linux-aarch64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-aarch64-3.9/khmer/_khmer.cpython-39-aarch64-linux-gnu.so -fopenmp building 'khmer._oxli.utils' extension creating build/temp.linux-aarch64-3.9/khmer creating build/temp.linux-aarch64-3.9/khmer/_oxli aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/khmer/_oxli/utils.o -O3 -std=c++11 -pedantic -fopenmp creating build/lib.linux-aarch64-3.9/khmer/_oxli aarch64-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-aarch64-3.9/khmer/_oxli/utils.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_utils.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-aarch64-3.9/src/oxli/read_parsers.o build/temp.linux-aarch64-3.9/src/oxli/kmer_hash.o build/temp.linux-aarch64-3.9/src/oxli/hashtable.o build/temp.linux-aarch64-3.9/src/oxli/hashgraph.o build/temp.linux-aarch64-3.9/src/oxli/labelhash.o build/temp.linux-aarch64-3.9/src/oxli/subset.o build/temp.linux-aarch64-3.9/src/oxli/read_aligner.o build/temp.linux-aarch64-3.9/src/oxli/hllcounter.o build/temp.linux-aarch64-3.9/src/oxli/traversal.o build/temp.linux-aarch64-3.9/src/oxli/kmer_filters.o build/temp.linux-aarch64-3.9/src/oxli/assembler.o build/temp.linux-aarch64-3.9/src/oxli/alphabets.o build/temp.linux-aarch64-3.9/src/oxli/storage.o build/temp.linux-aarch64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-aarch64-3.9/khmer/_oxli/utils.cpython-39-aarch64-linux-gnu.so -fopenmp building 'khmer._oxli.parsing' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-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-aarch64-3.9/khmer/_oxli/parsing.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_utils.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-aarch64-3.9/src/oxli/read_parsers.o build/temp.linux-aarch64-3.9/src/oxli/kmer_hash.o build/temp.linux-aarch64-3.9/src/oxli/hashtable.o build/temp.linux-aarch64-3.9/src/oxli/hashgraph.o build/temp.linux-aarch64-3.9/src/oxli/labelhash.o build/temp.linux-aarch64-3.9/src/oxli/subset.o build/temp.linux-aarch64-3.9/src/oxli/read_aligner.o build/temp.linux-aarch64-3.9/src/oxli/hllcounter.o build/temp.linux-aarch64-3.9/src/oxli/traversal.o build/temp.linux-aarch64-3.9/src/oxli/kmer_filters.o build/temp.linux-aarch64-3.9/src/oxli/assembler.o build/temp.linux-aarch64-3.9/src/oxli/alphabets.o build/temp.linux-aarch64-3.9/src/oxli/storage.o build/temp.linux-aarch64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-aarch64-3.9/khmer/_oxli/parsing.cpython-39-aarch64-linux-gnu.so -fopenmp building 'khmer._oxli.hashing' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/khmer/_oxli/hashing.o -O3 -std=c++11 -pedantic -fopenmp aarch64-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-aarch64-3.9/khmer/_oxli/hashing.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_utils.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-aarch64-3.9/src/oxli/read_parsers.o build/temp.linux-aarch64-3.9/src/oxli/kmer_hash.o build/temp.linux-aarch64-3.9/src/oxli/hashtable.o build/temp.linux-aarch64-3.9/src/oxli/hashgraph.o build/temp.linux-aarch64-3.9/src/oxli/labelhash.o build/temp.linux-aarch64-3.9/src/oxli/subset.o build/temp.linux-aarch64-3.9/src/oxli/read_aligner.o build/temp.linux-aarch64-3.9/src/oxli/hllcounter.o build/temp.linux-aarch64-3.9/src/oxli/traversal.o build/temp.linux-aarch64-3.9/src/oxli/kmer_filters.o build/temp.linux-aarch64-3.9/src/oxli/assembler.o build/temp.linux-aarch64-3.9/src/oxli/alphabets.o build/temp.linux-aarch64-3.9/src/oxli/storage.o build/temp.linux-aarch64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-aarch64-3.9/khmer/_oxli/hashing.cpython-39-aarch64-linux-gnu.so -fopenmp building 'khmer._oxli.graphs' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/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 | aarch64-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-aarch64-3.9/khmer/_oxli/graphs.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_utils.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-aarch64-3.9/src/oxli/read_parsers.o build/temp.linux-aarch64-3.9/src/oxli/kmer_hash.o build/temp.linux-aarch64-3.9/src/oxli/hashtable.o build/temp.linux-aarch64-3.9/src/oxli/hashgraph.o build/temp.linux-aarch64-3.9/src/oxli/labelhash.o build/temp.linux-aarch64-3.9/src/oxli/subset.o build/temp.linux-aarch64-3.9/src/oxli/read_aligner.o build/temp.linux-aarch64-3.9/src/oxli/hllcounter.o build/temp.linux-aarch64-3.9/src/oxli/traversal.o build/temp.linux-aarch64-3.9/src/oxli/kmer_filters.o build/temp.linux-aarch64-3.9/src/oxli/assembler.o build/temp.linux-aarch64-3.9/src/oxli/alphabets.o build/temp.linux-aarch64-3.9/src/oxli/storage.o build/temp.linux-aarch64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-aarch64-3.9/khmer/_oxli/graphs.cpython-39-aarch64-linux-gnu.so -fopenmp building 'khmer._oxli.assembly' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-aarch64-3.9/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 | aarch64-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-aarch64-3.9/khmer/_oxli/assembly.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_utils.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-aarch64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-aarch64-3.9/src/oxli/read_parsers.o build/temp.linux-aarch64-3.9/src/oxli/kmer_hash.o build/temp.linux-aarch64-3.9/src/oxli/hashtable.o build/temp.linux-aarch64-3.9/src/oxli/hashgraph.o build/temp.linux-aarch64-3.9/src/oxli/labelhash.o build/temp.linux-aarch64-3.9/src/oxli/subset.o build/temp.linux-aarch64-3.9/src/oxli/read_aligner.o build/temp.linux-aarch64-3.9/src/oxli/hllcounter.o build/temp.linux-aarch64-3.9/src/oxli/traversal.o build/temp.linux-aarch64-3.9/src/oxli/kmer_filters.o build/temp.linux-aarch64-3.9/src/oxli/assembler.o build/temp.linux-aarch64-3.9/src/oxli/alphabets.o build/temp.linux-aarch64-3.9/src/oxli/storage.o build/temp.linux-aarch64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-aarch64-3.9/khmer/_oxli/assembly.cpython-39-aarch64-linux-gnu.so -fopenmp copying build/lib.linux-aarch64-3.9/khmer/_khmer.cpython-39-aarch64-linux-gnu.so -> khmer copying build/lib.linux-aarch64-3.9/khmer/_oxli/utils.cpython-39-aarch64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-aarch64-3.9/khmer/_oxli/parsing.cpython-39-aarch64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-aarch64-3.9/khmer/_oxli/hashing.cpython-39-aarch64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-aarch64-3.9/khmer/_oxli/graphs.cpython-39-aarch64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-aarch64-3.9/khmer/_oxli/assembly.cpython-39-aarch64-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 aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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) : | ^~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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) { | ^~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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) { | ^~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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()); | ^~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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(); | ^~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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, | ^~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp aarch64-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-arm64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-arm64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-arm64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-arm64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-arm64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-arm64-3.9/src/khmer/_cpy_utils.o build/temp.linux-arm64-3.9/src/oxli/alphabets.o build/temp.linux-arm64-3.9/src/oxli/assembler.o build/temp.linux-arm64-3.9/src/oxli/hashgraph.o build/temp.linux-arm64-3.9/src/oxli/hashtable.o build/temp.linux-arm64-3.9/src/oxli/hllcounter.o build/temp.linux-arm64-3.9/src/oxli/kmer_filters.o build/temp.linux-arm64-3.9/src/oxli/kmer_hash.o build/temp.linux-arm64-3.9/src/oxli/labelhash.o build/temp.linux-arm64-3.9/src/oxli/read_aligner.o build/temp.linux-arm64-3.9/src/oxli/read_parsers.o build/temp.linux-arm64-3.9/src/oxli/storage.o build/temp.linux-arm64-3.9/src/oxli/subset.o build/temp.linux-arm64-3.9/src/oxli/traversal.o build/temp.linux-arm64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_khmer.cpython-39-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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 ; 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 224.16s (0:03:44) ==== rm -fr -- /tmp/dh-xdg-rundir-IMyF2HqH 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 aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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) : | ^~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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) { | ^~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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) { | ^~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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()); | ^~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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(); | ^~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/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, | ^~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/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-arm64-3.9/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp aarch64-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-arm64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-arm64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-arm64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-arm64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-arm64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-arm64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-arm64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-arm64-3.9/src/khmer/_cpy_utils.o build/temp.linux-arm64-3.9/src/oxli/alphabets.o build/temp.linux-arm64-3.9/src/oxli/assembler.o build/temp.linux-arm64-3.9/src/oxli/hashgraph.o build/temp.linux-arm64-3.9/src/oxli/hashtable.o build/temp.linux-arm64-3.9/src/oxli/hllcounter.o build/temp.linux-arm64-3.9/src/oxli/kmer_filters.o build/temp.linux-arm64-3.9/src/oxli/kmer_hash.o build/temp.linux-arm64-3.9/src/oxli/labelhash.o build/temp.linux-arm64-3.9/src/oxli/read_aligner.o build/temp.linux-arm64-3.9/src/oxli/read_parsers.o build/temp.linux-arm64-3.9/src/oxli/storage.o build/temp.linux-arm64-3.9/src/oxli/subset.o build/temp.linux-arm64-3.9/src/oxli/traversal.o build/temp.linux-arm64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_khmer.cpython-39-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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/aarch64-linux-gnu cp --reflink=auto -a ./src/oxli/liboxli.so.1 debian/liboxli1/usr/lib/aarch64-linux-gnu/ install -d debian/.debhelper/generated/liboxli1 install -d debian/liboxli-dev/usr/include/oxli cp --reflink=auto -a ./include/oxli/alphabets.hh ./include/oxli/assembler.hh ./include/oxli/hashgraph.hh ./include/oxli/hashtable.hh ./include/oxli/hllcounter.hh ./include/oxli/kmer_filters.hh ./include/oxli/kmer_hash.hh ./include/oxli/labelhash.hh ./include/oxli/oxli.hh ./include/oxli/oxli_exception.hh ./include/oxli/read_aligner.hh ./include/oxli/read_parsers.hh ./include/oxli/storage.hh ./include/oxli/subset.hh ./include/oxli/traversal.hh debian/liboxli-dev/usr/include/oxli/ install -d debian/liboxli-dev/usr/include/oxli/smhasher cp --reflink=auto -a ./third-party/smhasher/MurmurHash3.h debian/liboxli-dev/usr/include/oxli/smhasher/ install -d debian/liboxli-dev/usr/lib/aarch64-linux-gnu cp --reflink=auto -a ./src/oxli/liboxli.a ./src/oxli/liboxli.so debian/liboxli-dev/usr/lib/aarch64-linux-gnu/ install -d debian/liboxli-dev/usr/lib/aarch64-linux-gnu/pkgconfig cp --reflink=auto -a ./src/oxli/oxli.pc debian/liboxli-dev/usr/lib/aarch64-linux-gnu/pkgconfig/ install -d debian/.debhelper/generated/liboxli-dev find debian/khmer -name .gitignore -delete make[1]: Leaving directory '/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 dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js ln -sf ../../../../javascript/sphinxdoc/1.0/language_data.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js ln -sf ../../../../javascript/sphinxdoc/1.0/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 ln -sf ../../../../javascript/sphinxdoc/1.0/underscore.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js ln -sf ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/khmer-common/usr/share/doc/khmer-common/html/_static/labibi.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 (>= 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:Depends debian/khmer-common.substvars; echo "sphinxdoc:Depends=libjs-sphinxdoc (>= 1.0), 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: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/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/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/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 , 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/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/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/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 , 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/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/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/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 , 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/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/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/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 , 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/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/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/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 , 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/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/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/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 , 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/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/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/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 , 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/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 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 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:any', 'python3 (<< 3.10)', 'python3-screed (>= 1.0)', 'python3-bz2file', 'python3 (>= 3.9~)', '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/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/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/underscore.js ln -s ../../../../javascript/sphinxdoc/1.0/underscore.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js ln -s ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.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/aarch64-linux-gnu/liboxli.so ln -s liboxli.so.1 debian/liboxli-dev/usr/lib/aarch64-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/_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 Normalizing debian/khmer-common/usr/share/doc/khmer-common/html/_static/file.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/test-reads.fq.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fa.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.truncated.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/empty-file.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/goodversion-k12.ht.gz using File::StripNondeterminism::handlers::gzip dh_compress -O--buildsystem=pybuild cd debian/khmer-common cd debian/khmer cd debian/liboxli1 cd debian/liboxli-dev chmod a-x usr/share/doc/khmer-common/CITATION usr/share/doc/khmer-common/changelog usr/share/doc/khmer-common/changelog.Debian chmod a-x usr/share/doc/liboxli-dev/changelog usr/share/doc/liboxli-dev/changelog.Debian gzip -9nf usr/share/doc/khmer-common/CITATION usr/share/doc/khmer-common/changelog usr/share/doc/khmer-common/changelog.Debian gzip -9nf 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 cd '/build/khmer-2.1.2+dfsg' cd '/build/khmer-2.1.2+dfsg' gzip -9nf usr/share/doc/liboxli1/changelog usr/share/doc/liboxli1/changelog.Debian gzip -9nf usr/share/doc/khmer/changelog usr/share/doc/khmer/changelog.Debian usr/share/man/man1/khmer.1 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/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/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/liboxli-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/khmer/usr/share/doc -type f -a -true -a ! -regex 'debian/khmer/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli1/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/khmer-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/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 -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/share/man debian/khmer/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli1 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/khmer -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli1/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/khmer/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/khmer/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild install -d debian/khmer/usr/lib/debug/.dwz/aarch64-linux-gnu dwz -mdebian/khmer/usr/lib/debug/.dwz/aarch64-linux-gnu/khmer.debug -M/usr/lib/debug/.dwz/aarch64-linux-gnu/khmer.debug -- debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-39-aarch64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-39-aarch64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-39-aarch64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-39-aarch64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-39-aarch64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-39-aarch64-linux-gnu.so objcopy --compress-debug-sections debian/khmer/usr/lib/debug/.dwz/aarch64-linux-gnu/khmer.debug dwz -- debian/liboxli1/usr/lib/aarch64-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/aarch64-linux-gnu/liboxli.a install -d debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/f7 objcopy --only-keep-debug --compress-debug-sections debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/f7/ea4279604b809000df02da11a5338d36d92ac5.debug install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/8f objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-39-aarch64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/8f/d5e44921f8f03001224c026b39f784a6285580.debug chmod 0644 -- debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/f7/ea4279604b809000df02da11a5338d36d92ac5.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 objcopy --add-gnu-debuglink debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/f7/ea4279604b809000df02da11a5338d36d92ac5.debug debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/8f/d5e44921f8f03001224c026b39f784a6285580.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-39-aarch64-linux-gnu.so install -d debian/.debhelper/liboxli1/dbgsym-root/usr/share/doc ln -s liboxli1 debian/.debhelper/liboxli1/dbgsym-root/usr/share/doc/liboxli1-dbgsym objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/8f/d5e44921f8f03001224c026b39f784a6285580.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-39-aarch64-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/utils.cpython-39-aarch64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/23/1be045d6fc39bc1bb725583c414d37c35c1c18.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/23/1be045d6fc39bc1bb725583c414d37c35c1c18.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-39-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/23/1be045d6fc39bc1bb725583c414d37c35c1c18.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-39-aarch64-linux-gnu.so install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/86 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-39-aarch64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/86/d96ba27d10a52650ce47716cea55d27208aecf.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/86/d96ba27d10a52650ce47716cea55d27208aecf.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-39-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/86/d96ba27d10a52650ce47716cea55d27208aecf.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-39-aarch64-linux-gnu.so install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/34 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-39-aarch64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/34/949f0f5d1eac32e80ac1110b46745b9f4618a6.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/34/949f0f5d1eac32e80ac1110b46745b9f4618a6.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-39-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/34/949f0f5d1eac32e80ac1110b46745b9f4618a6.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-39-aarch64-linux-gnu.so install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/ea objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-39-aarch64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/ea/f27d56b4d87da43ea92cdc492ff7d5c1de528a.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/ea/f27d56b4d87da43ea92cdc492ff7d5c1de528a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-39-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/ea/f27d56b4d87da43ea92cdc492ff7d5c1de528a.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-39-aarch64-linux-gnu.so install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/c1 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-39-aarch64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/c1/75995001e4b28f9dca9298f89efcd81652fd71.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/c1/75995001e4b28f9dca9298f89efcd81652fd71.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-39-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/c1/75995001e4b28f9dca9298f89efcd81652fd71.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-39-aarch64-linux-gnu.so install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/khmer/usr/lib/debug/.dwz/aarch64-linux-gnu debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/khmer/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/khmer/usr/lib/debug install -d debian/.debhelper/khmer/dbgsym-root/usr/share/doc ln -s khmer debian/.debhelper/khmer/dbgsym-root/usr/share/doc/khmer-dbgsym dh_makeshlibs -a -O--buildsystem=pybuild rm -f debian/khmer/DEBIAN/shlibs rm -f debian/liboxli1/DEBIAN/shlibs install -d debian/liboxli1/DEBIAN echo "liboxli 1 liboxli1 (>= 2.1.2+dfsg)" >> debian/liboxli1/DEBIAN/shlibs chmod 0644 -- debian/liboxli1/DEBIAN/shlibs mv debian/.debhelper/generated/liboxli1/triggers.new debian/.debhelper/generated/liboxli1/triggers rm -f debian/liboxli-dev/DEBIAN/shlibs dh_shlibdeps -a -O--buildsystem=pybuild dpkg-shlibdeps -Tdebian/liboxli1.substvars debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 install -d debian/khmer/DEBIAN dpkg-shlibdeps -Tdebian/khmer.substvars debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-39-aarch64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-39-aarch64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-39-aarch64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-39-aarch64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-39-aarch64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-39-aarch64-linux-gnu.so dpkg-shlibdeps: warning: symbol gzread used by debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzclearerr used by debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gztell64 used by debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol BZ2_bzReadOpen used by debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzdopen used by debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzeof used by debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol deflate used by debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzopen64 used by debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol deflateEnd used by debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol deflateInit2_ used by debian/liboxli1/usr/lib/aarch64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: 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/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=f7ea4279604b809000df02da11a5338d36d92ac5 -DSection=debug -UReplaces -UBreaks 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=231be045d6fc39bc1bb725583c414d37c35c1c18 34949f0f5d1eac32e80ac1110b46745b9f4618a6 86d96ba27d10a52650ce47716cea55d27208aecf 8fd5e44921f8f03001224c026b39f784a6285580 c175995001e4b28f9dca9298f89efcd81652fd71 eaf27d56b4d87da43ea92cdc492ff7d5c1de528a" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/liboxli-dev/DEBIAN/control chmod 0644 -- debian/khmer-common/DEBIAN/control dpkg-gencontrol: warning: package khmer: substitution variable ${python3:Versions} unused, but is defined 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 chmod 0644 -- debian/liboxli1/DEBIAN/control dpkg-gencontrol: warning: package khmer: substitution variable ${python3:Versions} unused, but is defined chmod 0644 -- debian/khmer/DEBIAN/control dh_md5sums -O--buildsystem=pybuild cd debian/liboxli1 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/khmer >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/khmer-common >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/liboxli-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/liboxli1/DEBIAN/md5sums chmod 0644 -- debian/liboxli-dev/DEBIAN/md5sums cd debian/.debhelper/liboxli1/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/khmer-common/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/liboxli1/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/khmer/DEBIAN/md5sums cd debian/.debhelper/khmer/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/DEBIAN/md5sums dh_builddeb -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/khmer-common .. 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: building package 'khmer-common' in '../khmer-common_2.1.2+dfsg-8_all.deb'. dpkg-deb --root-owner-group --build debian/liboxli-dev .. dpkg-deb: building package 'khmer-dbgsym' in '../khmer-dbgsym_2.1.2+dfsg-8_arm64.deb'. dpkg-deb: building package 'khmer' in '../khmer_2.1.2+dfsg-8_arm64.deb'. dpkg-deb: building package 'liboxli1' in '../liboxli1_2.1.2+dfsg-8_arm64.deb'. dpkg-deb: building package 'liboxli1-dbgsym' in '../liboxli1-dbgsym_2.1.2+dfsg-8_arm64.deb'. dpkg-deb: building package 'liboxli-dev' in '../liboxli-dev_2.1.2+dfsg-8_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../khmer_2.1.2+dfsg-8_arm64.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: 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/21872 and its subdirectories I: Current time: Fri Aug 19 19:12:51 -12 2022 I: pbuilder-time-stamp: 1660979571 Sun Jul 18 00:49:56 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink16-arm64.debian.net. Sun Jul 18 00:49:56 UTC 2021 I: Preparing to do remote build '2' on codethink16-arm64.debian.net. Sun Jul 18 01:12:28 UTC 2021 I: Deleting $TMPDIR on codethink16-arm64.debian.net. Sun Jul 18 01:12:28 UTC 2021 I: khmer_2.1.2+dfsg-8_arm64.changes: Format: 1.8 Date: Mon, 04 Jan 2021 14:18:12 +0100 Source: khmer Binary: khmer khmer-common khmer-dbgsym liboxli-dev liboxli1 liboxli1-dbgsym Architecture: all arm64 Version: 2.1.2+dfsg-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: khmer - in-memory DNA sequence kmer counting, filtering & graph traversal khmer-common - common files for the khmer project tools liboxli-dev - in-memory DNA sequence analysis dev library liboxli1 - in-memory DNA sequence analysis library from the khmer project Changes: khmer (2.1.2+dfsg-8) unstable; urgency=medium . * Fix autopkgtests for newer pytest: s/pyarg/pyargs/ * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) * Update renamed lintian tag names in lintian overrides. * Replace use of deprecated $ADTTMP with $AUTOPKGTEST_TMP. Checksums-Sha1: 0b8446255a9178a9110a7b9f58ad92007c394d21 228204 khmer-common_2.1.2+dfsg-8_all.deb f271bb676d5a4ee3b7fc8ced629c7e74a7298359 15159100 khmer-dbgsym_2.1.2+dfsg-8_arm64.deb e017b1199ea1b4a118cd202608d5e880d07ba5ed 8967 khmer_2.1.2+dfsg-8_arm64.buildinfo 663e943e7745c70cf3046d84707521ea8b287069 6619292 khmer_2.1.2+dfsg-8_arm64.deb 3f9201a54b82b7d3ee00d2c4d18a56218ce910dd 268704 liboxli-dev_2.1.2+dfsg-8_arm64.deb 6de04332f3cf81b8d0582e25f52707ce73305387 2577152 liboxli1-dbgsym_2.1.2+dfsg-8_arm64.deb 5510c6eae4df9d813d4be3218baa221811f9b884 190852 liboxli1_2.1.2+dfsg-8_arm64.deb Checksums-Sha256: 928b7ad13d0291d708bd2b6c6798762e147a06840cd1c39e88e1ec9ab8683863 228204 khmer-common_2.1.2+dfsg-8_all.deb 44d8855bec4fdb40642135c1eb8e37c8d1c07e763228634e20fa40ce78ebdf30 15159100 khmer-dbgsym_2.1.2+dfsg-8_arm64.deb 0aa1a40a7fd1b787dd5172127d101d4757477d705d53e84ecaf2857458dd4d9a 8967 khmer_2.1.2+dfsg-8_arm64.buildinfo 640bed85da6dce72426ad38765754ab91a2e2e9839842191b0cfeb47946adbec 6619292 khmer_2.1.2+dfsg-8_arm64.deb c7b199e4c1c3c2c99aa6e752bf874baab63fca65cbeb9e28e381ffc7854eb55e 268704 liboxli-dev_2.1.2+dfsg-8_arm64.deb e33975742d9fd20495725f8fcf838524b33efc2b1c5ff90c1d543a52959f94db 2577152 liboxli1-dbgsym_2.1.2+dfsg-8_arm64.deb 4e9189bb84823880c9b219c05c7c9d871775d4c762a83231c32fd8b49f64f3c4 190852 liboxli1_2.1.2+dfsg-8_arm64.deb Files: c51a5412c044595a15f34277e5e20a1e 228204 science optional khmer-common_2.1.2+dfsg-8_all.deb e386d4927f845b70c0e12fe82f67b360 15159100 debug optional khmer-dbgsym_2.1.2+dfsg-8_arm64.deb 405e4c12367636f5d96e6c532f4f42d5 8967 science optional khmer_2.1.2+dfsg-8_arm64.buildinfo ce94a962550da22e25358adf6988debb 6619292 science optional khmer_2.1.2+dfsg-8_arm64.deb a423082065017edebd6966d4dd858caf 268704 libdevel optional liboxli-dev_2.1.2+dfsg-8_arm64.deb 6d1875ca9c3c06c52365293067212998 2577152 debug optional liboxli1-dbgsym_2.1.2+dfsg-8_arm64.deb 6b9ba39c6f358ad97e1746826031ef49 190852 libs optional liboxli1_2.1.2+dfsg-8_arm64.deb Sun Jul 18 01:12:30 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.uvpcoPqUCG/khmer_2.1.2+dfsg-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.uvpcoPqUCG/khmer_2.1.2+dfsg-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.uvpcoPqUCG/khmer_2.1.2+dfsg-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.uvpcoPqUCG/b1/khmer_2.1.2+dfsg-8_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.uvpcoPqUCG/b2/khmer_2.1.2+dfsg-8_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.674s) 0.674s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.294s) 0.294s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sun Jul 18 01:12:32 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Sun Jul 18 01:12:32 UTC 2021 I: khmer from bullseye built successfully and reproducibly on arm64. Sun Jul 18 01:12:34 UTC 2021 I: Submitting .buildinfo files to external archives: Sun Jul 18 01:12:34 UTC 2021 I: Submitting 12K b1/khmer_2.1.2+dfsg-8_arm64.buildinfo.asc Sun Jul 18 01:12:34 UTC 2021 I: Submitting 12K b2/khmer_2.1.2+dfsg-8_arm64.buildinfo.asc Sun Jul 18 01:12:36 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Jul 18 01:12:36 UTC 2021 I: Done submitting .buildinfo files. Sun Jul 18 01:12:36 UTC 2021 I: Removing signed khmer_2.1.2+dfsg-8_arm64.buildinfo.asc files: removed './b1/khmer_2.1.2+dfsg-8_arm64.buildinfo.asc' removed './b2/khmer_2.1.2+dfsg-8_arm64.buildinfo.asc'