Running as unit: rb-build-amd64_29-21299.service ==================================================================================== Sat Sep 28 13:18:42 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_29) on jenkins, called using "ionos1-amd64 ionos15-amd64" as arguments. Sat Sep 28 13:18:42 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-7zSkbnGH" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Sep 28 13:18:42 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Sat Sep 28 13:18:42 UTC 2024 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-i31JRE' Sat Sep 28 13:18:43 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Sat Sep 28 13:18:43 UTC 2024 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-qjH7A8' ok, let's check if khmer is building anywhere yet… ok, khmer is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of khmer in unstable on amd64 on jenkins now. 1st build will be done on ionos1-amd64.debian.net. 2nd build will be done on ionos15-amd64.debian.net. ============================================================================= Sat Sep 28 13:18:57 UTC 2024 I: starting to build khmer/unstable/amd64 on jenkins on '2024-09-28 13:18' Sat Sep 28 13:18:57 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_29/21299/console.log 1727529537 amd64 unstable khmer Sat Sep 28 13:18:57 UTC 2024 I: Downloading source for unstable/khmer=3.0.0~a3+dfsg-8 --2024-09-28 13:18:57-- http://deb.debian.org/debian/pool/main/k/khmer/khmer_3.0.0%7ea3%2bdfsg-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2565 (2.5K) [text/prs.lines.tag] Saving to: ‘khmer_3.0.0~a3+dfsg-8.dsc’ 0K .. 100% 366M=0s 2024-09-28 13:18:57 (366 MB/s) - ‘khmer_3.0.0~a3+dfsg-8.dsc’ saved [2565/2565] --2024-09-28 13:18:57-- http://deb.debian.org/debian/pool/main/k/khmer/khmer_3.0.0%7ea3%2bdfsg-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2565 (2.5K) [text/prs.lines.tag] Saving to: ‘khmer_3.0.0~a3+dfsg-8.dsc’ 0K .. 100% 366M=0s 2024-09-28 13:18:57 (366 MB/s) - ‘khmer_3.0.0~a3+dfsg-8.dsc’ saved [2565/2565] Sat Sep 28 13:18:57 UTC 2024 I: khmer_3.0.0~a3+dfsg-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: khmer Binary: khmer-common, khmer, liboxli1, liboxli-dev Architecture: all amd64 Version: 3.0.0~a3+dfsg-8 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Kevin Murray Homepage: https://khmer.readthedocs.org Standards-Version: 4.6.2 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-sequence-python3, dh-exec, python3-guzzle-sphinx-theme, python3, python3-dev, python3-all-dev, python3-setuptools, python3-screed, python3-pytest, python3-pytest-runner, python3-sphinx, python3-sphinxcontrib.autoprogram, cython3, zlib1g-dev, libbz2-dev, asciidoctor, rdfind Package-List: khmer deb science optional arch=amd64 khmer-common deb science optional arch=all liboxli-dev deb libdevel optional arch=amd64 liboxli1 deb libs optional arch=amd64 Checksums-Sha1: 1a51494aad337d08da8533335a797ea62524d55c 15748048 khmer_3.0.0~a3+dfsg.orig.tar.xz c95ce15d139766ec22035145b4df7dc83eb28d45 26572 khmer_3.0.0~a3+dfsg-8.debian.tar.xz Checksums-Sha256: c21d652ac412e641f568cdc300952d53620bb4902a9179c8267ea0030b799f75 15748048 khmer_3.0.0~a3+dfsg.orig.tar.xz 6dfb52b685a07473ea8cc1028f59d95f3f9cf7eaff7808d049d18713096d27ff 26572 khmer_3.0.0~a3+dfsg-8.debian.tar.xz Files: c89deeba6e3681cdf0218079abb9ebac 15748048 khmer_3.0.0~a3+dfsg.orig.tar.xz 5dd9c621331e99a9d67375f8e028a318 26572 khmer_3.0.0~a3+dfsg-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmXQnIYACgkQPCZ2P2xn 5uJzkg//Xtk8n+1/bLgQovM5DCVwjLyKaU08tCUL0soaS0ODegjfqFFs25i4DZyh QVNHhMQhLUSZCi6E1coEcWYk5wkOM6p9Y5pPtGGuQ2bWPlih5qDUUAIHiPenyAMK 5vEIi57SRIRkrCBybkPSOtYqpzXQYQ+GYztuxj6ZzucCigFgYY+WzAXamwZJha4x o4fKNeyo+c1HnN3CIiabcN6X+1mDyAL1ah1r+kYiwyJPpf68pFcDFTjYbUJXxykU g312qLhxPwKKkIbUmC15ZxGAZbyeYN6TXdQ0j6iXdMs4l7Nt8ia6pFFu3cMFoRtn 9TQudCZui7dojjn307tSmLzCP1aovnTIDrxYzQloHWa5XvEVYfPGRWrJ8S4y8f5X xMI6ihb9nC0AqsRKBzA2VkO5nlMsSdaRkwCV3ccCwC2cnqd7X+VJK/9FHd6CDCJH BuG7sGJGqmSWTGKkGkdGjFK9ea595ZyB0XvzxWf7ERd4zc2ww0LoYM/fymei3UVo JfgnS9RflxjZ35xsD75mHYBkip1+rjKqVEIVzmJ0wVvSLlRaWufT2ls9oU8niLAh vd3kcbJmtUKlHV3JvsWU8yrIk1L5gS+RzezE/xNt3YnOoI+7uKFr9U1Br/9RPz1m x5Mp+lVyI5XrLeIPsTiAdTLW6wBZfHLXinCFNKGHbwGWa9fJNGo= =Rz1f -----END PGP SIGNATURE----- Sat Sep 28 13:18:57 UTC 2024 I: Checking whether the package is not for us Sat Sep 28 13:18:57 UTC 2024 I: Starting 1st build on remote node ionos1-amd64.debian.net. Sat Sep 28 13:18:57 UTC 2024 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Sat Sep 28 13:18:57 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Sat Sep 28 13:18:57 UTC 2024 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-Bc5lj6' ==================================================================================== Sat Sep 28 13:18:58 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "1 khmer unstable /srv/reproducible-results/rbuild-debian/r-b-build.6173LJ7N 3.0.0~a3+dfsg-8" as arguments. Sat Sep 28 13:18:58 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-F3WXpbe3" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Sep 28 13:18:58 UTC 2024 I: Downloading source for unstable/khmer=3.0.0~a3+dfsg-8 Reading package lists... NOTICE: 'khmer' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/khmer.git Please use: git clone https://salsa.debian.org/med-team/khmer.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 15.8 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main khmer 3.0.0~a3+dfsg-8 (dsc) [2565 B] Get:2 http://deb.debian.org/debian unstable/main khmer 3.0.0~a3+dfsg-8 (tar) [15.7 MB] Get:3 http://deb.debian.org/debian unstable/main khmer 3.0.0~a3+dfsg-8 (diff) [26.6 kB] Fetched 15.8 MB in 0s (64.2 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'khmer' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/khmer.git Please use: git clone https://salsa.debian.org/med-team/khmer.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 15.8 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main khmer 3.0.0~a3+dfsg-8 (dsc) [2565 B] Get:2 http://deb.debian.org/debian unstable/main khmer 3.0.0~a3+dfsg-8 (tar) [15.7 MB] Get:3 http://deb.debian.org/debian unstable/main khmer 3.0.0~a3+dfsg-8 (diff) [26.6 kB] Fetched 15.8 MB in 0s (64.2 MB/s) Download complete and in download only mode ============================================================================= Building khmer in unstable on amd64 on ionos1-amd64 now. Date: Sat Sep 28 13:18:59 UTC 2024 Date UTC: Sat Sep 28 13:18:59 UTC 2024 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Sat Sep 28 01:18:59 -12 2024 I: pbuilder-time-stamp: 1727529539 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [khmer_3.0.0~a3+dfsg-8.dsc] I: copying [./khmer_3.0.0~a3+dfsg.orig.tar.xz] I: copying [./khmer_3.0.0~a3+dfsg-8.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Feb 17 11:46:14 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./khmer_3.0.0~a3+dfsg-8.dsc: no acceptable signature found dpkg-source: info: extracting khmer in khmer-3.0.0~a3+dfsg dpkg-source: info: unpacking khmer_3.0.0~a3+dfsg.orig.tar.xz dpkg-source: info: unpacking khmer_3.0.0~a3+dfsg-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying nose2pytest dpkg-source: info: applying fix_non_x86_build dpkg-source: info: applying hardening dpkg-source: info: applying update-manifest dpkg-source: info: applying setup-py-py3 dpkg-source: info: applying local-libs dpkg-source: info: applying older-setuptools dpkg-source: info: applying disable_google_analytics dpkg-source: info: applying get_version dpkg-source: info: applying install-prefix dpkg-source: info: applying cpython-bug-empty-exceptions dpkg-source: info: applying amend-skip dpkg-source: info: applying python3 dpkg-source: info: applying fix_liboxli_test dpkg-source: info: applying gcc11.patch dpkg-source: info: applying bz2.patch dpkg-source: info: applying stringio-buffer.patch dpkg-source: info: applying refresh_cython dpkg-source: info: applying find_object_files_at_right_loc.patch dpkg-source: info: applying python3.12-support.patch dpkg-source: info: applying close-opened-files.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2070678/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='500224182994485195b2535b62c00cc0' 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='2070678' 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/r-b-build.6173LJ7N/pbuilderrc_ohbD --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6173LJ7N/b1 --logfile b1/build.log khmer_3.0.0~a3+dfsg-8.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.106-3 (2024-08-26) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2070678/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, dh-exec, python3-guzzle-sphinx-theme, python3, python3-dev, python3-all-dev, python3-setuptools, python3-screed, python3-pytest, python3-pytest-runner, python3-sphinx, python3-sphinxcontrib.autoprogram, cython3, zlib1g-dev, libbz2-dev, asciidoctor, rdfind dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19787 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-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on python3-guzzle-sphinx-theme; however: Package python3-guzzle-sphinx-theme is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-screed; however: Package python3-screed is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-runner; however: Package python3-pytest-runner is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.autoprogram; however: Package python3-sphinxcontrib.autoprogram is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor is not installed. pbuilder-satisfydepends-dummy depends on rdfind; however: Package rdfind is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fonts-glyphicons-halflings{a} fonts-liberation{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbz2-dev{a} libcom-err2{a} libdebhelper-perl{a} libedit2{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libicu72{a} libjs-bootstrap{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnsl2{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} libruby{a} libruby3.1t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-guzzle-sphinx-theme{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pygments{a} python3-pytest{a} python3-pytest-runner{a} python3-requests{a} python3-roman{a} python3-screed{a} python3-setuptools{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinxcontrib.autoprogram{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} rake{a} rdfind{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl fonts-lato fonts-liberation-sans-narrow javascript-common krb5-locales libarchive-cpio-perl libgpm2 libjson-xs-perl libltdl-dev libmail-sendmail-perl libpaper-utils lynx python3-pil wget zip 0 packages upgraded, 131 newly installed, 0 to remove and 0 not upgraded. Need to get 62.0 MB of archives. After unpacking 259 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.6-1 [814 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.3-1 [105 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 12 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.3.2-1 [1381 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-8 [97.3 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.18 [6704 B] Get: 37 http://deb.debian.org/debian unstable/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 ruby-sdbm amd64 1.0.0-5+b4 [15.4 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libruby3.1t64 amd64 3.1.2-8.4 [5411 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 ruby3.1 amd64 3.1.2-8.4 [664 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.1+nmu1 [4664 B] Get: 48 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.1+nmu1 [5584 B] Get: 50 http://deb.debian.org/debian unstable/main amd64 ruby-asciidoctor all 2.0.23-1 [214 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 asciidoctor all 2.0.23-1 [88.7 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 cython3 amd64 3.0.11+dfsg-1 [2449 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 64 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 dh-exec amd64 0.30 [25.6 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.4.0-1 [63.7 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 79 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 74.1.2-2 [736 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240824 [109 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 fonts-liberation all 1:2.1.5-3 [1475 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.3-1 [157 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.4.7-3 [158 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.6-1 [2147 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.6-1 [5127 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.12.6-1 [9952 B] Get: 99 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.12.6-1 [1064 B] Get: 100 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.12.6-1 [1040 B] Get: 103 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.6-1 [506 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.12.6-1 [26.1 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.12.6-1 [1068 B] Get: 106 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.14.0-1 [111 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2024.8.30-1 [159 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.3.2-4 [117 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 python3-roman all 4.2-1 [10.4 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 7.4.7-3 [731 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 115 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b1 [13.6 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.1-1 [45.8 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.8-2 [41.6 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.0.7-2 [111 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 7.4.7-3 [588 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 python3-guzzle-sphinx-theme all 0.7.11-6 [1346 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 126 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.3.3-1 [249 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 python3-pytest-runner all 2.11.1-4 [8432 B] Get: 129 http://deb.debian.org/debian unstable/main amd64 python3-screed all 1.1.3-1 [109 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.autoprogram all 0.1.9-1 [10.6 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 rdfind amd64 1.6.0-1+b1 [44.7 kB] Fetched 62.0 MB in 1s (72.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19787 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.6-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_amd64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:amd64 (3.12.6-1) ... Setting up libexpat1:amd64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... 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 ... 20107 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_amd64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... 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 ... 21179 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.3.2-1_amd64.deb ... Unpacking openssl (3.3.2-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../006-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../009-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.40.2-8_amd64.deb ... Unpacking bsdextrautils (2.40.2-8) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../012-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... 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Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up python-babel-localedata (2.14.0-1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Sep 28 13:20:20 UTC 2024. Universal Time is now: Sat Sep 28 13:20:20 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libexpat1-dev:amd64 (2.6.3-1) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up autoconf (2.72-3) ... Setting up ruby-webrick (1.8.1-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libjson-perl (4.10000-1) ... Setting up fonts-liberation (1:2.1.5-3) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up openssl (3.3.2-1) ... Setting up readline-common (8.2-5) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libjs-sphinxdoc (7.4.7-3) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up sphinx-common (7.4.7-3) ... Setting up libnsl2:amd64 (1.3.0-3+b2) ... Setting up libpython3.12-stdlib:amd64 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up debhelper (13.20) ... Setting up dh-exec (0.30) ... Setting up libpython3.12t64:amd64 (3.12.6-1) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up libpython3.12-dev:amd64 (3.12.6-1) ... Setting up python3-zipp (3.20.2-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b1) ... Setting up python3-roman (4.2-1) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.1-1) ... Setting up python3-certifi (2024.8.30-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up python3-idna (3.8-2) ... Setting up python3.12-dev (3.12.6-1) ... Setting up cython3 (3.0.11+dfsg-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-urllib3 (2.0.7-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-more-itertools (10.4.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up libpython3-dev:amd64 (3.12.6-1) ... Setting up python3-jaraco.functools (4.0.2-1) ... Setting up python3-screed (1.1.3-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-charset-normalizer (3.3.2-4) ... Setting up python3-pytest (8.3.3-1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-all (3.12.6-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up libpython3-all-dev:amd64 (3.12.6-1) ... Setting up python3-dev (3.12.6-1) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-all-dev (3.12.6-1) ... Setting up python3-setuptools (74.1.2-2) ... Setting up python3-babel (2.14.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-pytest-runner (2.11.1-4) ... Setting up dh-python (6.20240824) ... Setting up rake (13.2.1-1) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b4) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up libruby3.1t64:amd64 (3.1.2-8.4) ... Setting up ruby3.1 (3.1.2-8.4) ... Setting up libruby:amd64 (1:3.1+nmu1) ... Setting up ruby (1:3.1+nmu1) ... Setting up ruby-asciidoctor (2.0.23-1) ... Setting up asciidoctor (2.0.23-1) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (7.4.7-3) ... Setting up python3-guzzle-sphinx-theme (0.7.11-6) ... Setting up python3-sphinxcontrib.autoprogram (0.1.9-1) ... Processing triggers for ca-certificates (20240203) ... 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/reproducible-path/khmer-3.0.0~a3+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_3.0.0~a3+dfsg-8_source.changes dpkg-buildpackage: info: source package khmer dpkg-buildpackage: info: source version 3.0.0~a3+dfsg-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg' dh_auto_clean || /bin/true pybuild --clean -i python{version} -p 3.12 I: pybuild base:311: python3.12 setup.py clean /build/reproducible-path/khmer-3.0.0~a3+dfsg/versioneer.py:421: SyntaxWarning: invalid escape sequence '\s' LONG_VERSION_PY['git'] = ''' *** NOTE: Found Cython, extension files will be transpiled if this is an install invocation. /usr/lib/python3/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) /usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) /usr/lib/python3/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running clean removing '/build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.12' 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/reproducible-path/khmer-3.0.0~a3+dfsg/src/oxli' (cd ../../third-party/cqf && make clean) make[3]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' rm -f *.o gqf.o make[3]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' rm -f *.o *.a *.so* oxli.pc make[2]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/src/oxli' rm -rf __pycache__ .eggs make[1]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/khmer-common.substvars debian/khmer.substvars debian/liboxli1.substvars debian/liboxli-dev.substvars ./khmer/_oxli/assembly.cpp ./khmer/_oxli/graphs.cpp ./khmer/_oxli/hashing.cpp ./khmer/_oxli/hashset.cpp ./khmer/_oxli/hllcounter.cpp ./khmer/_oxli/labeling.cpp ./khmer/_oxli/legacy_partitioning.cpp ./khmer/_oxli/parsing.cpp ./khmer/_oxli/readaligner.cpp ./khmer/_oxli/traversal.cpp ./khmer/_oxli/utils.cpp debian/files rm -fr -- debian/khmer-common/ debian/tmp/ debian/khmer/ debian/liboxli1/ debian/liboxli-dev/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --with sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild pybuild --configure -i python{version} -p 3.12 I: pybuild base:311: python3.12 setup.py config /build/reproducible-path/khmer-3.0.0~a3+dfsg/versioneer.py:421: SyntaxWarning: invalid escape sequence '\s' LONG_VERSION_PY['git'] = ''' *** NOTE: Found Cython, extension files will be transpiled if this is an install invocation. /usr/lib/python3/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) /usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) /usr/lib/python3/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg' dh_auto_build pybuild --build -i python{version} -p 3.12 I: pybuild base:311: /usr/bin/python3 setup.py build *** NOTE: Found Cython, extension files will be transpiled if this is an install invocation. /usr/lib/python3/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) /usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) /usr/lib/python3/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running build running build_py creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer copying khmer/kfile.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer copying khmer/khmer_logger.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer copying khmer/khmer_args.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer copying khmer/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer copying khmer/trimming.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer copying khmer/utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer copying khmer/_version.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer copying khmer/thread_utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_lump.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_memory.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_oxli_functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_qfstorage.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_nibblestorage.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_subset_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_version.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_read_handling.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_sequence_validation.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_script_output.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_read_parsers.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_sandbox_scripts.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_normalize_by_median.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_scripts.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_hashset.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_banding.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_counttable.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_script_arguments.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/graph_features.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_cython_parsing.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_threaded_sequence_processor.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_hll.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_counting_single.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_countgraph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_tabletype.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_labelhash.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_cpython_hierarchy.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_read_aligner.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_filter_abund.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/khmer_tst_utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_assembly.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_nodegraph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/table_fixtures.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_streaming_io.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli copying oxli/build_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli copying oxli/partition.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli copying oxli/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli copying oxli/functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_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' dependency include/oxli/khmer.hh won't be automatically included in the manifest: the path doesn't exist reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.cpp' under directory 'khmer/_oxli' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'khmer.egg-info/SOURCES.txt' copying tests/.gitignore -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.truncated.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.truncated.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/README.rst -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/all-A.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k12.ct -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k12.ht -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k32.stoptags -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k32.tagset -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/banding-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/biglump-random-20-a.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/bogus.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/branched-genome.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/casava_18-pe.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/combine_parts_1.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-all-paired-all-keep.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-none-paired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-some-paired-all-keep.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/fakelump.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/fakelump.fa.stoptags.txt -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/filter-test-A.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/filter-test-B.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k12.ht -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k12.ht.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k32.stoptags -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k32.tagset -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/multi-output.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/normC20k20.ct -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/old-style-format-w-comments.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.badleft -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.badright -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.paired_bad -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken2.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken2.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken3.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken3.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken4.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken4.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-2.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-broken.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-witherror.fa.pe -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa.pe -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa.se -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq.pe -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq.se -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired.malformat.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired.malformat.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired_one.base.dif.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-X2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.even.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.part -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.odd.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-b.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-31-c.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/readaligner-default.json -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/readaligner-k12.json -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/real-partition-small.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/real-partition-tiny.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/seq-a.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/seq-b.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/simple-genome-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/simple-genome.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/single-read.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/single-read.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.paired.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.paired2.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-3.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-impaired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-paired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-paired.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-empty.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-empty.fa.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-error-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-n-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-filter-abund-Ns.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph5.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-labels.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-large.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-multi.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-output-partitions.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-overlap1.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-overlap2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fq.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fq.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-short.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-contigs.fp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-transcript.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/truncated.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/unclean-reads.fastq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/valid-read-testing.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying khmer/_oxli/assembly.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/assembly.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/hashset.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/hashset.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/hllcounter.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/hllcounter.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/labeling.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/labeling.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/legacy_partitioning.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/legacy_partitioning.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/oxli_exception_convert.cc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/oxli_exception_convert.hh -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/oxli_types.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/readaligner.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/readaligner.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/traversal.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/traversal.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/utils.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/utils.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli UPDATING /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_version.py set /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_version.py to '3.0.0a3' running build_ext bash -c "cd third-party/cqf && make" make[2]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' g++ -std=c++11 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Ofast -I. -Wno-unused-result -Wno-strict-aliasing -Wno-unused-function gqf.c -c -o gqf.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ make[2]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' building 'khmer._khmer' extension creating build creating build/temp.linux-x86_64-cpython-312 creating build/temp.linux-x86_64-cpython-312/src creating build/temp.linux-x86_64-cpython-312/src/khmer creating build/temp.linux-x86_64-cpython-312/src/oxli creating build/temp.linux-x86_64-cpython-312/third-party creating build/temp.linux-x86_64-cpython-312/third-party/smhasher x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o -O3 -std=c++11 -fopenmp In file included from third-party/seqan/core/include/seqan/basic.h:62, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:40: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/modifier.h:66, from third-party/seqan/core/include/seqan/file.h:48, from third-party/seqan/core/include/seqan/stream.h:70, from third-party/seqan/core/include/seqan/seq_io.h:45: third-party/seqan/core/include/seqan/modifier/modifier_functors.h:68:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 68 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from src/oxli/read_parsers.cc:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:91:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 91 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:115:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 115 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:169:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 169 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:178:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 178 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:188:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 188 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:198:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 198 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:208:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 208 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:217:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 217 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:229:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/file.h:117: third-party/seqan/core/include/seqan/file/string_external.h:1316:51: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1316 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/graph_algorithms.h:46, from third-party/seqan/core/include/seqan/graph_align.h:47, from third-party/seqan/core/include/seqan/align.h:54, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83: third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:340:23: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 340 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/graph_algorithms.h:47: third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm.h:643:23: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 643 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:79: third-party/seqan/core/include/seqan/align/gap_anchor.h:246:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/align/gap_anchor.h:256:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:59: third-party/seqan/core/include/seqan/store/store_align.h:322:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 322 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:332:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 332 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:342:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 342 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:352:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:362:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:372:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/storage.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/subset.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_khmer.cpython-312-x86_64-linux-gnu.so -fopenmp Compiling khmer/_oxli/hashing.pyx because it changed. [1/1] Cythonizing khmer/_oxli/hashing.pyx building 'khmer._oxli.hashing' extension creating build/temp.linux-x86_64-cpython-312/khmer creating build/temp.linux-x86_64-cpython-312/khmer/_oxli x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/hashing.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/hashing.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/hashing.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hashing.cpython-312-x86_64-linux-gnu.so -fopenmp warning: khmer/_oxli/parsing.pxd:60:20: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:61:31: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:78:21: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:79:32: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. Compiling khmer/_oxli/assembly.pyx because it changed. [1/1] Cythonizing khmer/_oxli/assembly.pyx building 'khmer._oxli.assembly' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/assembly.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/assembly.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:1334: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/assembly.cpp:1206:11: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/assembly.cpp:1215:11: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/assembly.cpp:1212:11: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/assembly.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/assembly.cpython-312-x86_64-linux-gnu.so -fopenmp warning: khmer/_oxli/parsing.pxd:60:20: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:61:31: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:78:21: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:79:32: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. Compiling khmer/_oxli/legacy_partitioning.pyx because it changed. [1/1] Cythonizing khmer/_oxli/legacy_partitioning.pyx building 'khmer._oxli.legacy_partitioning' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/legacy_partitioning.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/legacy_partitioning.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/legacy_partitioning.cpp:1333: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/legacy_partitioning.cpp:1205:11: note: this is the location of the previous definition 1205 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/legacy_partitioning.cpp:1214:11: note: this is the location of the previous definition 1214 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/legacy_partitioning.cpp:1211:11: note: this is the location of the previous definition 1211 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/legacy_partitioning.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/legacy_partitioning.cpython-312-x86_64-linux-gnu.so -fopenmp Compiling khmer/_oxli/hashset.pyx because it changed. [1/1] Cythonizing khmer/_oxli/hashset.pyx building 'khmer._oxli.hashset' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/hashset.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/hashset.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/hashset.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hashset.cpython-312-x86_64-linux-gnu.so -fopenmp warning: khmer/_oxli/parsing.pxd:60:20: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:61:31: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:78:21: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:79:32: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. Compiling khmer/_oxli/parsing.pyx because it changed. [1/1] Cythonizing khmer/_oxli/parsing.pyx building 'khmer._oxli.parsing' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/parsing.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/parsing.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/parsing.cpp:1321: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/parsing.cpp:1199:11: note: this is the location of the previous definition 1199 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/parsing.cpp:1208:11: note: this is the location of the previous definition 1208 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:1205:11: note: this is the location of the previous definition 1205 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/parsing.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/parsing.cpython-312-x86_64-linux-gnu.so -fopenmp Compiling khmer/_oxli/utils.pyx because it changed. [1/1] Cythonizing khmer/_oxli/utils.pyx building 'khmer._oxli.utils' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/utils.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/utils.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/utils.cpython-312-x86_64-linux-gnu.so -fopenmp warning: khmer/_oxli/parsing.pxd:60:20: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:61:31: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:78:21: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:79:32: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. Compiling khmer/_oxli/labeling.pyx because it changed. [1/1] Cythonizing khmer/_oxli/labeling.pyx building 'khmer._oxli.labeling' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/labeling.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/labeling.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/labeling.cpp:1333: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/labeling.cpp:1205:11: note: this is the location of the previous definition 1205 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/labeling.cpp:1214:11: note: this is the location of the previous definition 1214 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/labeling.cpp:1211:11: note: this is the location of the previous definition 1211 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/labeling.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/labeling.cpython-312-x86_64-linux-gnu.so -fopenmp warning: khmer/_oxli/parsing.pxd:60:20: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:61:31: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:78:21: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:79:32: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. Compiling khmer/_oxli/readaligner.pyx because it changed. [1/1] Cythonizing khmer/_oxli/readaligner.pyx building 'khmer._oxli.readaligner' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/readaligner.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/readaligner.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/readaligner.cpp:1334: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/readaligner.cpp:1206:11: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/readaligner.cpp:1215:11: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/readaligner.cpp:1212:11: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/readaligner.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/readaligner.cpython-312-x86_64-linux-gnu.so -fopenmp warning: khmer/_oxli/parsing.pxd:60:20: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:61:31: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:78:21: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:79:32: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. Compiling khmer/_oxli/graphs.pyx because it changed. [1/1] Cythonizing khmer/_oxli/graphs.pyx building 'khmer._oxli.graphs' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/graphs.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/graphs.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:1334: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/graphs.cpp:1206:11: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/graphs.cpp:1215:11: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/graphs.cpp:1212:11: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/graphs.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/graphs.cpython-312-x86_64-linux-gnu.so -fopenmp warning: khmer/_oxli/parsing.pxd:60:20: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:61:31: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:78:21: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:79:32: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. Compiling khmer/_oxli/traversal.pyx because it changed. [1/1] Cythonizing khmer/_oxli/traversal.pyx building 'khmer._oxli.traversal' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/traversal.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/traversal.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/traversal.cpp:1334: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/traversal.cpp:1206:11: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/traversal.cpp:1215:11: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/traversal.cpp:1212:11: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/traversal.cpython-312-x86_64-linux-gnu.so -fopenmp warning: khmer/_oxli/parsing.pxd:60:20: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:61:31: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:78:21: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:79:32: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. Compiling khmer/_oxli/hllcounter.pyx because it changed. [1/1] Cythonizing khmer/_oxli/hllcounter.pyx building 'khmer._oxli.hllcounter' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/hllcounter.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/hllcounter.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/hllcounter.cpp:1327: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/hllcounter.cpp:1201:11: note: this is the location of the previous definition 1201 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/hllcounter.cpp:1210:11: note: this is the location of the previous definition 1210 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/hllcounter.cpp:1207:11: note: this is the location of the previous definition 1207 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hllcounter.cpython-312-x86_64-linux-gnu.so -fopenmp running build_scripts creating build/scripts-3.12 copying and adjusting scripts/unique-kmers.py -> build/scripts-3.12 copying and adjusting scripts/count-median.py -> build/scripts-3.12 copying and adjusting scripts/load-into-counting.py -> build/scripts-3.12 copying and adjusting scripts/normalize-by-median.py -> build/scripts-3.12 copying and adjusting scripts/make-initial-stoptags.py -> build/scripts-3.12 copying and adjusting scripts/extract-paired-reads.py -> build/scripts-3.12 copying and adjusting scripts/sample-reads-randomly.py -> build/scripts-3.12 copying and adjusting scripts/abundance-dist.py -> build/scripts-3.12 copying and adjusting scripts/partition-graph.py -> build/scripts-3.12 copying and adjusting scripts/extract-partitions.py -> build/scripts-3.12 copying and adjusting scripts/filter-abund.py -> build/scripts-3.12 copying and adjusting scripts/readstats.py -> build/scripts-3.12 copying and adjusting scripts/trim-low-abund.py -> build/scripts-3.12 copying and adjusting scripts/merge-partitions.py -> build/scripts-3.12 copying and adjusting scripts/abundance-dist-single.py -> build/scripts-3.12 copying and adjusting scripts/interleave-reads.py -> build/scripts-3.12 copying and adjusting scripts/find-knots.py -> build/scripts-3.12 copying and adjusting scripts/fastq-to-fasta.py -> build/scripts-3.12 copying and adjusting scripts/load-graph.py -> build/scripts-3.12 copying and adjusting scripts/extract-long-sequences.py -> build/scripts-3.12 copying and adjusting scripts/split-paired-reads.py -> build/scripts-3.12 copying and adjusting scripts/do-partition.py -> build/scripts-3.12 copying and adjusting scripts/annotate-partitions.py -> build/scripts-3.12 copying and adjusting scripts/filter-stoptags.py -> build/scripts-3.12 copying and adjusting scripts/filter-abund-single.py -> build/scripts-3.12 changing mode of build/scripts-3.12/unique-kmers.py from 644 to 755 changing mode of build/scripts-3.12/count-median.py from 644 to 755 changing mode of build/scripts-3.12/load-into-counting.py from 644 to 755 changing mode of build/scripts-3.12/normalize-by-median.py from 644 to 755 changing mode of build/scripts-3.12/make-initial-stoptags.py from 644 to 755 changing mode of build/scripts-3.12/extract-paired-reads.py from 644 to 755 changing mode of build/scripts-3.12/sample-reads-randomly.py from 644 to 755 changing mode of build/scripts-3.12/abundance-dist.py from 644 to 755 changing mode of build/scripts-3.12/partition-graph.py from 644 to 755 changing mode of build/scripts-3.12/extract-partitions.py from 644 to 755 changing mode of build/scripts-3.12/filter-abund.py from 644 to 755 changing mode of build/scripts-3.12/readstats.py from 644 to 755 changing mode of build/scripts-3.12/trim-low-abund.py from 644 to 755 changing mode of build/scripts-3.12/merge-partitions.py from 644 to 755 changing mode of build/scripts-3.12/abundance-dist-single.py from 644 to 755 changing mode of build/scripts-3.12/interleave-reads.py from 644 to 755 changing mode of build/scripts-3.12/find-knots.py from 644 to 755 changing mode of build/scripts-3.12/fastq-to-fasta.py from 644 to 755 changing mode of build/scripts-3.12/load-graph.py from 644 to 755 changing mode of build/scripts-3.12/extract-long-sequences.py from 644 to 755 changing mode of build/scripts-3.12/split-paired-reads.py from 644 to 755 changing mode of build/scripts-3.12/do-partition.py from 644 to 755 changing mode of build/scripts-3.12/annotate-partitions.py from 644 to 755 changing mode of build/scripts-3.12/filter-stoptags.py from 644 to 755 changing mode of build/scripts-3.12/filter-abund-single.py from 644 to 755 ln -sf `pybuild --print build_dir|awk -F: '{print $2}'`/khmer/*.so khmer && \ ./setup.py develop --user && sphinx-build doc build/sphinx/html *** NOTE: Found Cython, extension files will be transpiled if this is an install invocation. /usr/lib/python3/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) /usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) /usr/lib/python3/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running develop /usr/lib/python3/dist-packages/setuptools/command/develop.py:41: EasyInstallDeprecationWarning: easy_install command is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` and ``easy_install``. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://github.com/pypa/setuptools/issues/917 for details. ******************************************************************************** !! easy_install.initialize_options(self) /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() 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 dependency include/oxli/khmer.hh won't be automatically included in the manifest: the path doesn't exist reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'khmer.egg-info/SOURCES.txt' running build_ext bash -c "cd third-party/cqf && make" make[2]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' building 'khmer._khmer' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o -O3 -std=c++11 -fopenmp In file included from third-party/seqan/core/include/seqan/basic.h:62, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:40: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/modifier.h:66, from third-party/seqan/core/include/seqan/file.h:48, from third-party/seqan/core/include/seqan/stream.h:70, from third-party/seqan/core/include/seqan/seq_io.h:45: third-party/seqan/core/include/seqan/modifier/modifier_functors.h:68:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 68 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from src/oxli/read_parsers.cc:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:91:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 91 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:115:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 115 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:169:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 169 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:178:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 178 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:188:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 188 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:198:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 198 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:208:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 208 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:217:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 217 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:229:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/file.h:117: third-party/seqan/core/include/seqan/file/string_external.h:1316:51: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1316 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/graph_algorithms.h:46, from third-party/seqan/core/include/seqan/graph_align.h:47, from third-party/seqan/core/include/seqan/align.h:54, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83: third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:340:23: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 340 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/graph_algorithms.h:47: third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm.h:643:23: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 643 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:79: third-party/seqan/core/include/seqan/align/gap_anchor.h:246:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/align/gap_anchor.h:256:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:59: third-party/seqan/core/include/seqan/store/store_align.h:322:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 322 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:332:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 332 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:342:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 342 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:352:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:362:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:372:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/storage.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/subset.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -fopenmp creating build/lib.linux-x86_64-cpython-312 creating build/lib.linux-x86_64-cpython-312/khmer x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_khmer.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hashing' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/hashing.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/hashing.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp creating build/lib.linux-x86_64-cpython-312/khmer/_oxli x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/hashing.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/hashing.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.assembly' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/assembly.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/assembly.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:1334: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/assembly.cpp:1206:11: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/assembly.cpp:1215:11: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/assembly.cpp:1212:11: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/assembly.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/assembly.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.legacy_partitioning' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/legacy_partitioning.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/legacy_partitioning.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/legacy_partitioning.cpp:1333: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/legacy_partitioning.cpp:1205:11: note: this is the location of the previous definition 1205 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/legacy_partitioning.cpp:1214:11: note: this is the location of the previous definition 1214 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/legacy_partitioning.cpp:1211:11: note: this is the location of the previous definition 1211 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/legacy_partitioning.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/legacy_partitioning.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hashset' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/hashset.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/hashset.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/hashset.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/hashset.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.parsing' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/parsing.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/parsing.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/parsing.cpp:1321: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/parsing.cpp:1199:11: note: this is the location of the previous definition 1199 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/parsing.cpp:1208:11: note: this is the location of the previous definition 1208 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:1205:11: note: this is the location of the previous definition 1205 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/parsing.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/parsing.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.utils' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/utils.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/utils.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/utils.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.labeling' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/labeling.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/labeling.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/labeling.cpp:1333: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/labeling.cpp:1205:11: note: this is the location of the previous definition 1205 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/labeling.cpp:1214:11: note: this is the location of the previous definition 1214 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/labeling.cpp:1211:11: note: this is the location of the previous definition 1211 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/labeling.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/labeling.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.readaligner' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/readaligner.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/readaligner.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/readaligner.cpp:1334: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/readaligner.cpp:1206:11: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/readaligner.cpp:1215:11: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/readaligner.cpp:1212:11: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/readaligner.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/readaligner.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.graphs' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/graphs.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/graphs.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:1334: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/graphs.cpp:1206:11: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/graphs.cpp:1215:11: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/graphs.cpp:1212:11: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/graphs.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/graphs.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.traversal' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/traversal.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/traversal.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/traversal.cpp:1334: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/traversal.cpp:1206:11: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/traversal.cpp:1215:11: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/traversal.cpp:1212:11: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/traversal.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hllcounter' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/hllcounter.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/hllcounter.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/hllcounter.cpp:1327: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/hllcounter.cpp:1201:11: note: this is the location of the previous definition 1201 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/hllcounter.cpp:1210:11: note: this is the location of the previous definition 1210 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/hllcounter.cpp:1207:11: note: this is the location of the previous definition 1207 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/hllcounter.cpython-312-x86_64-linux-gnu.so -fopenmp copying build/lib.linux-x86_64-cpython-312/khmer/_khmer.cpython-312-x86_64-linux-gnu.so -> khmer copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/hashing.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/assembly.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/legacy_partitioning.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/hashset.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/parsing.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/utils.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/labeling.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/readaligner.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/graphs.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/traversal.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/hllcounter.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli Creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/lib/python3.12/site-packages/khmer.egg-link (link to .) Adding khmer 3.0.0a3 to easy-install.pth file Installing unique-kmers.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing count-median.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing load-into-counting.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing normalize-by-median.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing make-initial-stoptags.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing extract-paired-reads.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing sample-reads-randomly.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing abundance-dist.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing partition-graph.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing extract-partitions.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing filter-abund.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing readstats.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing trim-low-abund.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing merge-partitions.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing abundance-dist-single.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing interleave-reads.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing find-knots.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing fastq-to-fasta.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing load-graph.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing extract-long-sequences.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing split-paired-reads.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing do-partition.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing annotate-partitions.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing filter-stoptags.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing filter-abund-single.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installed /build/reproducible-path/khmer-3.0.0~a3+dfsg Processing dependencies for khmer==3.0.0a3 Searching for screed==1.1.3 Best match: screed 1.1.3 Adding screed 1.1.3 to easy-install.pth file Installing screed script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Using /usr/lib/python3/dist-packages Finished processing dependencies for khmer==3.0.0a3 Running Sphinx v7.4.7 loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 41 source files that are out of date updating environment: [new config] 41 added, 0 changed, 0 removed reading sources... 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[100%] user/scripts looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/khmer-3.0.0~a3+dfsg/doc/dev/hackathon.rst: WARNING: document isn't included in any toctree /build/reproducible-path/khmer-3.0.0~a3+dfsg/doc/dev/python-api.rst: WARNING: document isn't included in any toctree done preparing documents... done copying assets... copying static files... done copying extra files... done copying assets: done writing output... [ 2%] LICENSE writing output... [ 5%] citations writing output... [ 7%] contributors writing output... [ 10%] dev/CODE_OF_CONDUCT writing output... [ 12%] dev/a-quick-guide-to-testing writing output... [ 15%] dev/binary-file-formats writing output... [ 17%] dev/codebase-guide writing output... [ 20%] dev/development writing output... [ 22%] dev/for-khmer-developers writing output... [ 24%] dev/getting-started writing output... [ 27%] dev/guidelines-continued-dev writing output... 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[100%] user/scripts /build/reproducible-path/khmer-3.0.0~a3+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: 'load-into-counting.py -N' /build/reproducible-path/khmer-3.0.0~a3+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: 'load-into-counting.py --n_tables' /build/reproducible-path/khmer-3.0.0~a3+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: 'load-into-counting.py -x' /build/reproducible-path/khmer-3.0.0~a3+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: 'load-into-counting.py --max-tablesize' /build/reproducible-path/khmer-3.0.0~a3+dfsg/doc/user/scripts.rst:79: WARNING: unknown option: '-x' /build/reproducible-path/khmer-3.0.0~a3+dfsg/doc/user/scripts.rst:79: WARNING: unknown option: '-N' /build/reproducible-path/khmer-3.0.0~a3+dfsg/doc/user/scripts.rst:87: WARNING: unknown option: '-x' /build/reproducible-path/khmer-3.0.0~a3+dfsg/doc/user/scripts.rst:87: WARNING: unknown option: '-N' generating indices... genindex done writing additional pages... search done copying images... 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The HTML pages are in build/sphinx/html. asciidoctor --backend manpage -a reproducible debian/khmer.1.adoc /usr/bin/make -C src/oxli clean make[2]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/src/oxli' (cd ../../third-party/cqf && make clean) make[3]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' rm -f *.o gqf.o make[3]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' rm -f *.o *.a *.so* oxli.pc make[2]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/src/oxli' /usr/bin/make -C src/oxli all USE_SYSTEM_ZLIB="true" USE_SYSTEM_LIBBZ2="true" make[2]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/src/oxli' (cd ../../third-party/cqf && make) make[3]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' g++ -std=c++11 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wshadow -Wcast-align -Wstrict-prototypes -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -fopenmp -DNO_UNIQUE_RC=0 -Wall -Ofast -I. -Wno-unused-result -Wno-strict-aliasing -Wno-unused-function gqf.c -c -o gqf.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: command-line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ gqf.c: In function 'void remove_replace_slots_and_shift_remainders_and_runends_and_offsets(QF*, int, uint64_t, uint64_t, const uint64_t*, uint64_t, uint64_t)': gqf.c:789:34: warning: declaration of 'i' shadows a previous local [-Wshadow] 789 | uint64_t i; | ^ gqf.c:748:18: note: shadowed declaration is here 748 | uint64_t i; | ^ gqf.c:834:42: warning: declaration of 'i' shadows a previous local [-Wshadow] 834 | uint64_t i; | ^ gqf.c:748:18: note: shadowed declaration is here 748 | uint64_t i; | ^ make[3]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o hashtable.o hashtable.cc hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': hashtable.cc:626:1: required from here 626 | ); | ^ hashtable.cc:138:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 138 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': hashtable.cc:643:1: required from here 643 | ); | ^ hashtable.cc:208:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 208 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_with_mask(oxli::read_parsers::ReadParserPtr&, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': hashtable.cc:662:1: required from here 662 | ); | ^ hashtable.cc:168:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 168 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding_with_mask(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': hashtable.cc:685:1: required from here 685 | ); | ^ hashtable.cc:250:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 250 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from hashtable.cc:49: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o hashgraph.o hashgraph.cc In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from ../../include/oxli/hashgraph.hh:52, from hashgraph.cc:47: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o hllcounter.o hllcounter.cc hllcounter.cc: In instantiation of 'void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': hllcounter.cc:435:1: required from here 435 | ); | ^ hllcounter.cc:366:40: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 366 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from hllcounter.cc:48: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o kmer_hash.o kmer_hash.cc In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from kmer_hash.cc:49: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o labelhash.o labelhash.cc In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from ../../include/oxli/hashgraph.hh:52, from labelhash.cc:44: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o traversal.o traversal.cc In file included from traversal.cc:39: traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]': traversal.cc:202:5: required from here 202 | left_gatherer(ht, filters), | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ../../include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ ../../include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]': traversal.cc:203:5: required from here 203 | right_gatherer(ht, filters) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ ../../include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from traversal.cc:38: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o read_aligner.o read_aligner.cc In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from read_aligner.cc:46: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from read_aligner.cc:48: ../../include/oxli/read_aligner.hh:114:15: warning: 'oxli::freq_default' defined but not used [-Wunused-variable] 114 | static double freq_default[] = { log2(0.955), | ^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o read_parsers.o read_parsers.cc In file included from ../../third-party/seqan/core/include/seqan/basic.h:62, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:40: ../../third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from ../../third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/modifier.h:66, from ../../third-party/seqan/core/include/seqan/file.h:48, from ../../third-party/seqan/core/include/seqan/stream.h:70, from ../../third-party/seqan/core/include/seqan/seq_io.h:45: ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:68:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 68 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from read_parsers.cc:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:91:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 91 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:115:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 115 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:169:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 169 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:178:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 178 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:188:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 188 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:198:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 198 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:208:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 208 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:217:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 217 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:229:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/file.h:117: ../../third-party/seqan/core/include/seqan/file/string_external.h:1316:51: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1316 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/graph_algorithms.h:46, from ../../third-party/seqan/core/include/seqan/graph_align.h:47, from ../../third-party/seqan/core/include/seqan/align.h:54, from ../../third-party/seqan/core/include/seqan/store.h:38, from ../../third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from ../../third-party/seqan/core/include/seqan/seq_io.h:83: ../../third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:340:23: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 340 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/graph_algorithms.h:47: ../../third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm.h:643:23: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 643 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/align.h:79: ../../third-party/seqan/core/include/seqan/align/gap_anchor.h:246:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/align/gap_anchor.h:256:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/align.h:116: ../../third-party/seqan/core/include/seqan/align/dp_cell_affine.h: In member function 'seqan::DPCell_ >& seqan::DPCell_ >::operator=(const seqan::DPCell_ >&)': ../../third-party/seqan/core/include/seqan/align/dp_cell_affine.h:84:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 84 | if (this != &other) | ^~ ../../third-party/seqan/core/include/seqan/align/dp_cell_affine.h:86:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 86 | _horizontalScore = other._horizontalScore; | ^~~~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/align.h:166: ../../third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function 'int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)': ../../third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ ../../third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from ../../third-party/seqan/core/include/seqan/align.h:174: ../../third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function 'seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)': ../../third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ ../../third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from ../../third-party/seqan/core/include/seqan/bam_io.h:107, from ../../third-party/seqan/core/include/seqan/store.h:41: ../../third-party/seqan/core/include/seqan/bam_io/bam_stream.h: At global scope: ../../third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/store.h:59: ../../third-party/seqan/core/include/seqan/store/store_align.h:322:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 322 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/store/store_align.h:332:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 332 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/store/store_align.h:342:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 342 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/store/store_align.h:352:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/store/store_align.h:362:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/store/store_align.h:372:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/store.h:61: ../../third-party/seqan/core/include/seqan/store/store_all.h: In function 'void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)': ../../third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 1733 | if (alignQualityStoreLengthPre == 0u) | ^~ ../../third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o subset.o subset.cc subset.cc: In member function 'size_t oxli::SubsetPartition::output_partitioned_file(const std::string&, const std::string&, bool, oxli::CallbackFn, void*)': subset.cc:136:24: warning: unused variable 'ksize' [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from ../../include/oxli/hashgraph.hh:52, from subset.cc:47: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o kmer_filters.o kmer_filters.cc In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from kmer_filters.cc:40: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o assembler.o assembler.cc In file included from assembler.cc:38: ../../include/oxli/assembler.hh: In constructor 'oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)': ../../include/oxli/assembler.hh:80:23: warning: 'oxli::LinearAssembler::graph' will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ ../../include/oxli/assembler.hh:79:16: warning: 'oxli::WordLength oxli::LinearAssembler::_ksize' [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ assembler.cc: In destructor 'oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()': assembler.cc:189:5: warning: deleting object of polymorphic class type 'oxli::LinearAssembler' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ ../../include/oxli/assembler.hh: In constructor 'oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)': ../../include/oxli/assembler.hh:158:16: warning: 'oxli::JunctionCountAssembler::_ksize' will be initialized after [-Wreorder] 158 | WordLength _ksize; | ^~~~~~ ../../include/oxli/assembler.hh:153:15: warning: 'oxli::Traverser oxli::JunctionCountAssembler::traverser' [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ ../../include/oxli/assembler.hh:153:15: warning: 'oxli::JunctionCountAssembler::traverser' will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ ../../include/oxli/assembler.hh:151:21: warning: 'oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm' [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/assembler.hh:43: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o alphabets.o alphabets.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -c -o murmur3.o ../../third-party/smhasher/MurmurHash3.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o storage.o storage.cc In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from storage.cc:44: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -Wl,-soname=liboxli.so.1 -shared -o liboxli.so.1 hashtable.o hashgraph.o hllcounter.o kmer_hash.o labelhash.o traversal.o read_aligner.o read_parsers.o subset.o kmer_filters.o assembler.o alphabets.o murmur3.o storage.o ../../third-party/cqf/gqf.o ln -sf liboxli.so.1 liboxli.so ar rcs liboxli.a hashtable.o hashgraph.o hllcounter.o kmer_hash.o labelhash.o traversal.o read_aligner.o read_parsers.o subset.o kmer_filters.o assembler.o alphabets.o murmur3.o storage.o ../../third-party/cqf/gqf.o ranlib liboxli.a sed -e 's,@prefix@,/usr/local,' -e 's,@VERSION@,,' oxli.pc.in >oxli.pc make[2]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/src/oxli' make[1]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg' rm -f debian/khmer-common.debhelper.log debian/khmer.debhelper.log debian/liboxli-dev.debhelper.log debian/liboxli1.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg' dh_auto_install install -m0755 -d /build/reproducible-path/khmer-3.0.0\~a3\+dfsg/debian/tmp pybuild --install -i python{version} -p 3.12 --dest-dir /build/reproducible-path/khmer-3.0.0\~a3\+dfsg/debian/tmp I: pybuild base:311: /usr/bin/python3 setup.py install --root '/build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer' '--install-scripts=/usr/lib/khmer/bin' *** NOTE: Found Cython, extension files will be transpiled if this is an install invocation. /usr/lib/python3/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) /usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) /usr/lib/python3/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() 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 dependency include/oxli/khmer.hh won't be automatically included in the manifest: the path doesn't exist reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'khmer.egg-info/SOURCES.txt' copying khmer/_oxli/assembly.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/hashset.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/hllcounter.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/labeling.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/legacy_partitioning.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/readaligner.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/traversal.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/utils.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli UPDATING /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_version.py set /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_version.py to '3.0.0a3' running build_ext bash -c "cd third-party/cqf && make" make[2]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' building 'khmer._khmer' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o -O3 -std=c++11 -fopenmp In file included from third-party/seqan/core/include/seqan/basic.h:62, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:40: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/modifier.h:66, from third-party/seqan/core/include/seqan/file.h:48, from third-party/seqan/core/include/seqan/stream.h:70, from third-party/seqan/core/include/seqan/seq_io.h:45: third-party/seqan/core/include/seqan/modifier/modifier_functors.h:68:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 68 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from src/oxli/read_parsers.cc:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:91:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 91 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:115:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 115 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:169:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 169 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:178:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 178 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:188:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 188 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:198:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 198 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:208:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 208 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:217:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 217 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:229:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/file.h:117: third-party/seqan/core/include/seqan/file/string_external.h:1316:51: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1316 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/graph_algorithms.h:46, from third-party/seqan/core/include/seqan/graph_align.h:47, from third-party/seqan/core/include/seqan/align.h:54, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83: third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:340:23: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 340 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/graph_algorithms.h:47: third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm.h:643:23: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 643 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:79: third-party/seqan/core/include/seqan/align/gap_anchor.h:246:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/align/gap_anchor.h:256:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:59: third-party/seqan/core/include/seqan/store/store_align.h:322:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 322 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:332:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 332 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:342:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 342 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:352:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:362:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:372:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/storage.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/subset.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_khmer.cpython-312-x86_64-linux-gnu.so -fopenmp running build_scripts running install_lib creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12 creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli/build_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli/partition.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli/functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/kfile.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/khmer_logger.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/khmer_args.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_lump.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_memory.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_oxli_functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_qfstorage.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_nibblestorage.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/.gitignore -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_subset_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_version.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_read_handling.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_sequence_validation.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_script_output.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_read_parsers.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_sandbox_scripts.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_normalize_by_median.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_scripts.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_hashset.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_banding.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_counttable.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_script_arguments.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/graph_features.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_cython_parsing.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_threaded_sequence_processor.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_hll.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_counting_single.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_countgraph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_tabletype.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_labelhash.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_cpython_hierarchy.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-output-partitions.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/100-reads.fq.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/old-style-format-w-comments.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/100-reads.fq.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/badversion-k12.ht -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-reads.fq.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-slash1.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-mixed.fq.pe -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/README.rst -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-error-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/simple-genome.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired.malformat.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-fastq-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read-impaired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired.fa.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/badversion-k32.tagset -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken4.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/filter-test-A.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-X2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read-2.paired2.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-short.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-sweep-contigs.fp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken3.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-mixed-witherror.fa.pe -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/empty-file.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken2.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/truncated.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-graph5.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-mixed.fa.se -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/normC20k20.ct -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-large.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired.fa.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/real-partition-small.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/simple-genome-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-mixed.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-mixed-2.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/dn-test-some-paired-all-keep.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-fastq-n-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/goodversion-k32.tagset -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-labels.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-slash1.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-a.even.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-overlap1.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/filter-test-B.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/banding-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken4.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-overlap2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-a.fa.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-empty.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/multi-output.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-sweep-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/bogus.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-a.odd.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/biglump-random-20-a.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/empty-file -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/badversion-k32.stoptags -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-mixed.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/fakelump.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/dn-test-all-paired-all-keep.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/all-A.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/single-read.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-sweep-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read-paired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read-3.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/empty-file.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/badversion-k12.ct -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/dn-test-none-paired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/seq-b.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-a.fq.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-a.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-reads.fq.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-31-c.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/casava_18-pe.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-mixed.fa.pe -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-filter-abund-Ns.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken.fq.paired_bad -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-empty.fa.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-graph.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-a.fa.part -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/unclean-reads.fastq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/real-partition-tiny.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-multi.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-a.fa.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/branched-genome.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read-2.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired_one.base.dif.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/goodversion-k12.ht -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-fastq-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-mixed-broken.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/seq-a.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-mixed.fq.se -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/readaligner-k12.json -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/readaligner-default.json -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-a.fq.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-b.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-a.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired.malformat.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/goodversion-k12.ht.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/single-read.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-graph2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/combine_parts_1.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read-paired.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/goodversion-k32.stoptags -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read-2.paired.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/fakelump.fa.stoptags.txt -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-transcript.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-slash1.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken2.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/valid-read-testing.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read-2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken.fq.badright -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken.fq.badleft -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken3.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_read_aligner.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_filter_abund.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/khmer_tst_utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_assembly.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_nodegraph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/table_fixtures.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_streaming_io.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_khmer.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/trimming.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hllcounter.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/legacy_partitioning.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/parsing.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/utils.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hllcounter.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/graphs.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/oxli_exception_convert.cc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/assembly.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hashing.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/assembly.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/legacy_partitioning.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/utils.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hashing.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hashing.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hashset.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/parsing.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/readaligner.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/utils.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hashing.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/parsing.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/assembly.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/assembly.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/oxli_exception_convert.hh -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/labeling.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/traversal.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hashset.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/graphs.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/traversal.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/oxli_types.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/readaligner.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/labeling.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/graphs.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/labeling.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/readaligner.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/traversal.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/labeling.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/graphs.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/traversal.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/utils.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hashset.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hashset.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/parsing.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hllcounter.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hllcounter.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/readaligner.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/legacy_partitioning.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/legacy_partitioning.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_version.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/thread_utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli/build_graph.py to build_graph.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli/partition.py to partition.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli/functions.py to functions.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/kfile.py to kfile.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/khmer_logger.py to khmer_logger.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/khmer_args.py to khmer_args.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_lump.py to test_lump.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_memory.py to test_memory.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_oxli_functions.py to test_oxli_functions.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_qfstorage.py to test_qfstorage.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_nibblestorage.py to test_nibblestorage.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_subset_graph.py to test_subset_graph.cpython-312.pyc /usr/lib/python3.12/dist-packages/khmer/tests/test_subset_graph.py:61: SyntaxWarning: "is" with 'int' literal. Did you mean "=="? /usr/lib/python3.12/dist-packages/khmer/tests/test_subset_graph.py:82: SyntaxWarning: "is" with 'int' literal. Did you mean "=="? /usr/lib/python3.12/dist-packages/khmer/tests/test_subset_graph.py:278: SyntaxWarning: "is" with 'int' literal. Did you mean "=="? /usr/lib/python3.12/dist-packages/khmer/tests/test_subset_graph.py:476: SyntaxWarning: "is" with 'int' literal. Did you mean "=="? /usr/lib/python3.12/dist-packages/khmer/tests/test_subset_graph.py:509: SyntaxWarning: "is" with 'int' literal. Did you mean "=="? byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_functions.py to test_functions.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_version.py to test_version.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_read_handling.py to test_read_handling.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_sequence_validation.py to test_sequence_validation.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_script_output.py to test_script_output.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_read_parsers.py to test_read_parsers.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_sandbox_scripts.py to test_sandbox_scripts.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_normalize_by_median.py to test_normalize_by_median.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_scripts.py to test_scripts.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_hashset.py to test_hashset.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_banding.py to test_banding.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_counttable.py to test_counttable.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_script_arguments.py to test_script_arguments.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/graph_features.py to graph_features.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_cython_parsing.py to test_cython_parsing.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_threaded_sequence_processor.py to test_threaded_sequence_processor.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_hll.py to test_hll.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_counting_single.py to test_counting_single.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_countgraph.py to test_countgraph.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_tabletype.py to test_tabletype.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_labelhash.py to test_labelhash.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_cpython_hierarchy.py to test_cpython_hierarchy.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_read_aligner.py to test_read_aligner.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_filter_abund.py to test_filter_abund.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_graph.py to test_graph.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/khmer_tst_utils.py to khmer_tst_utils.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_assembly.py to test_assembly.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_nodegraph.py to test_nodegraph.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/table_fixtures.py to table_fixtures.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_streaming_io.py to test_streaming_io.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/trimming.py to trimming.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/utils.py to utils.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_version.py to _version.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/thread_utils.py to thread_utils.cpython-312.pyc running install_egg_info Copying khmer.egg-info to /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer-3.0.0a3.egg-info Skipping SOURCES.txt running install_scripts creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/unique-kmers.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/count-median.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/load-into-counting.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/normalize-by-median.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/make-initial-stoptags.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/extract-paired-reads.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/sample-reads-randomly.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/abundance-dist.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/partition-graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/extract-partitions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/filter-abund.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/readstats.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/trim-low-abund.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/merge-partitions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/abundance-dist-single.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/interleave-reads.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/find-knots.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/fastq-to-fasta.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/load-graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/extract-long-sequences.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/split-paired-reads.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/do-partition.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/annotate-partitions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/filter-stoptags.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/filter-abund-single.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/unique-kmers.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/count-median.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/load-into-counting.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/normalize-by-median.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/make-initial-stoptags.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/extract-paired-reads.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/sample-reads-randomly.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/abundance-dist.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/partition-graph.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/extract-partitions.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/filter-abund.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/readstats.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/trim-low-abund.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/merge-partitions.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/abundance-dist-single.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/interleave-reads.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/find-knots.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/fastq-to-fasta.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/load-graph.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/extract-long-sequences.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/split-paired-reads.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/do-partition.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/annotate-partitions.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/filter-stoptags.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/filter-abund-single.py to 755 PYBUILD_SYSTEM=custom \ PYBUILD_TEST_ARGS="cd {dir}; export PATH={destdir}/usr/lib/khmer/bin:$PATH ; \ cd {build_dir}; export PYTHONPATH=$(pwd); {interpreter} -m pytest \ -m 'not known_failing and not jenkins and not huge and not noroot'\ -q" dh_auto_test pybuild --test --test-pytest -i python{version} -p 3.12 I: pybuild base:311: cd '/build/reproducible-path/khmer-3.0.0~a3+dfsg'; export PATH='/build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer'/usr/lib/khmer/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games ; cd '/build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build'; export PYTHONPATH=/build/reproducible-path/khmer-3.0.0~a3+dfsg; python3.12 -m pytest -m 'not known_failing and not jenkins and not huge and not noroot' -q ============================= test session starts ============================== platform linux -- Python 3.12.6, pytest-8.3.3, pluggy-1.5.0 rootdir: /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build configfile: pytest.ini testpaths: tests plugins: typeguard-4.3.0 collected 1492 items / 47 deselected / 1445 selected tests/test_assembly.py ................................................. [ 3%] ........................................................................ [ 8%] ........................................................................ [ 13%] ..........................................X............................. [ 18%] ........................................................................ [ 23%] .................... [ 24%] tests/test_banding.py ............ [ 25%] tests/test_countgraph.py ........Fatal Python error: Aborted Current thread 0x00007f7fefc8e080 (most recent call first): File "/build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/tests/test_countgraph.py", line 212 in test_get_raw_tables_smallcountgraph File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159 in pytest_pyfunc_call File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627 in runtest File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174 in pytest_runtest_call File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242 in File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341 in from_call File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 241 in call_and_report File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 132 in runtestprotocol File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 113 in pytest_runtest_protocol File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ File "/usr/lib/python3/dist-packages/_pytest/main.py", line 362 in pytest_runtestloop File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ File "/usr/lib/python3/dist-packages/_pytest/main.py", line 337 in _main File "/usr/lib/python3/dist-packages/_pytest/main.py", line 283 in wrap_session File "/usr/lib/python3/dist-packages/_pytest/main.py", line 330 in pytest_cmdline_main File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 175 in main File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 201 in console_main File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 9 in File "", line 88 in _run_code File "", line 198 in _run_module_as_main Extension modules: khmer._khmer, khmer._oxli.hashing, khmer._oxli.utils, khmer._oxli.parsing, khmer._oxli.hashset, khmer._oxli.traversal, khmer._oxli.graphs, khmer._oxli.legacy_partitioning, khmer._oxli.labeling, khmer._oxli.assembly, khmer._oxli.readaligner, khmer._oxli.hllcounter (total: 12) Aborted E: pybuild pybuild:389: test: plugin custom failed with: exit code=134: cd '/build/reproducible-path/khmer-3.0.0~a3+dfsg'; export PATH='/build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer'/usr/lib/khmer/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games ; cd '/build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build'; export PYTHONPATH=/build/reproducible-path/khmer-3.0.0~a3+dfsg; python3.12 -m pytest -m 'not known_failing and not jenkins and not huge and not noroot' -q rm -fr -- /tmp/dh-xdg-rundir-mJozUTkN dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.12 returned exit code 13 make[1]: *** [debian/rules:29: override_dh_auto_test] Error 25 make[1]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg' make: *** [debian/rules:16: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/2070678 and its subdirectories Starting cleanup. All cleanup done. Sat Sep 28 13:34:48 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-F3WXpbe3, removing. /srv/reproducible-results/rbuild-debian/r-b-build.6173LJ7N: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Sep 28 13:34 b1 drwxr-xr-x 2 jenkins jenkins 4096 Sep 28 13:18 b2 -rw-r--r-- 1 jenkins jenkins 2565 Feb 17 2024 khmer_3.0.0~a3+dfsg-8.dsc -rw------- 1 jenkins jenkins 3695 Sep 28 13:18 rbuildlog.IfT9YR0 /srv/reproducible-results/rbuild-debian/r-b-build.6173LJ7N/b1: total 424 -rw-r--r-- 1 jenkins jenkins 433002 Sep 28 13:34 build.log /srv/reproducible-results/rbuild-debian/r-b-build.6173LJ7N/b2: total 0 Sat Sep 28 13:34:49 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Sep 28 01:18:59 -12 2024 I: pbuilder-time-stamp: 1727529539 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [khmer_3.0.0~a3+dfsg-8.dsc] I: copying [./khmer_3.0.0~a3+dfsg.orig.tar.xz] I: copying [./khmer_3.0.0~a3+dfsg-8.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Feb 17 11:46:14 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./khmer_3.0.0~a3+dfsg-8.dsc: no acceptable signature found dpkg-source: info: extracting khmer in khmer-3.0.0~a3+dfsg dpkg-source: info: unpacking khmer_3.0.0~a3+dfsg.orig.tar.xz dpkg-source: info: unpacking khmer_3.0.0~a3+dfsg-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying nose2pytest dpkg-source: info: applying fix_non_x86_build dpkg-source: info: applying hardening dpkg-source: info: applying update-manifest dpkg-source: info: applying setup-py-py3 dpkg-source: info: applying local-libs dpkg-source: info: applying older-setuptools dpkg-source: info: applying disable_google_analytics dpkg-source: info: applying get_version dpkg-source: info: applying install-prefix dpkg-source: info: applying cpython-bug-empty-exceptions dpkg-source: info: applying amend-skip dpkg-source: info: applying python3 dpkg-source: info: applying fix_liboxli_test dpkg-source: info: applying gcc11.patch dpkg-source: info: applying bz2.patch dpkg-source: info: applying stringio-buffer.patch dpkg-source: info: applying refresh_cython dpkg-source: info: applying find_object_files_at_right_loc.patch dpkg-source: info: applying python3.12-support.patch dpkg-source: info: applying close-opened-files.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2070678/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='500224182994485195b2535b62c00cc0' 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='2070678' 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/r-b-build.6173LJ7N/pbuilderrc_ohbD --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6173LJ7N/b1 --logfile b1/build.log khmer_3.0.0~a3+dfsg-8.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.106-3 (2024-08-26) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2070678/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, dh-exec, python3-guzzle-sphinx-theme, python3, python3-dev, python3-all-dev, python3-setuptools, python3-screed, python3-pytest, python3-pytest-runner, python3-sphinx, python3-sphinxcontrib.autoprogram, cython3, zlib1g-dev, libbz2-dev, asciidoctor, rdfind dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19787 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-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on python3-guzzle-sphinx-theme; however: Package python3-guzzle-sphinx-theme is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-screed; however: Package python3-screed is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-runner; however: Package python3-pytest-runner is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.autoprogram; however: Package python3-sphinxcontrib.autoprogram is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor is not installed. pbuilder-satisfydepends-dummy depends on rdfind; however: Package rdfind is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fonts-glyphicons-halflings{a} fonts-liberation{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbz2-dev{a} libcom-err2{a} libdebhelper-perl{a} libedit2{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libicu72{a} libjs-bootstrap{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnsl2{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} libruby{a} libruby3.1t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-guzzle-sphinx-theme{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pygments{a} python3-pytest{a} python3-pytest-runner{a} python3-requests{a} python3-roman{a} python3-screed{a} python3-setuptools{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinxcontrib.autoprogram{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} rake{a} rdfind{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl fonts-lato fonts-liberation-sans-narrow javascript-common krb5-locales libarchive-cpio-perl libgpm2 libjson-xs-perl libltdl-dev libmail-sendmail-perl libpaper-utils lynx python3-pil wget zip 0 packages upgraded, 131 newly installed, 0 to remove and 0 not upgraded. Need to get 62.0 MB of archives. After unpacking 259 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.6-1 [814 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.3-1 [105 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 12 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.3.2-1 [1381 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-8 [97.3 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.18 [6704 B] Get: 37 http://deb.debian.org/debian unstable/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 ruby-sdbm amd64 1.0.0-5+b4 [15.4 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libruby3.1t64 amd64 3.1.2-8.4 [5411 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 ruby3.1 amd64 3.1.2-8.4 [664 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.1+nmu1 [4664 B] Get: 48 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.1+nmu1 [5584 B] Get: 50 http://deb.debian.org/debian unstable/main amd64 ruby-asciidoctor all 2.0.23-1 [214 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 asciidoctor all 2.0.23-1 [88.7 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 cython3 amd64 3.0.11+dfsg-1 [2449 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 64 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 dh-exec amd64 0.30 [25.6 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.4.0-1 [63.7 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 79 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 74.1.2-2 [736 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240824 [109 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 fonts-liberation all 1:2.1.5-3 [1475 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.3-1 [157 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.4.7-3 [158 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.6-1 [2147 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.6-1 [5127 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.12.6-1 [9952 B] Get: 99 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.12.6-1 [1064 B] Get: 100 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.12.6-1 [1040 B] Get: 103 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.6-1 [506 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.12.6-1 [26.1 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.12.6-1 [1068 B] Get: 106 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.14.0-1 [111 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2024.8.30-1 [159 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.3.2-4 [117 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 python3-roman all 4.2-1 [10.4 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 7.4.7-3 [731 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 115 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b1 [13.6 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.1-1 [45.8 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.8-2 [41.6 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.0.7-2 [111 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 7.4.7-3 [588 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 python3-guzzle-sphinx-theme all 0.7.11-6 [1346 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 126 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.3.3-1 [249 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 python3-pytest-runner all 2.11.1-4 [8432 B] Get: 129 http://deb.debian.org/debian unstable/main amd64 python3-screed all 1.1.3-1 [109 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.autoprogram all 0.1.9-1 [10.6 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 rdfind amd64 1.6.0-1+b1 [44.7 kB] Fetched 62.0 MB in 1s (72.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19787 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.6-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_amd64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:amd64 (3.12.6-1) ... Setting up libexpat1:amd64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... 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 ... 20107 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_amd64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... 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 ... 21179 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sgml-base. 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Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up python-babel-localedata (2.14.0-1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Sep 28 13:20:20 UTC 2024. Universal Time is now: Sat Sep 28 13:20:20 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libexpat1-dev:amd64 (2.6.3-1) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up autoconf (2.72-3) ... Setting up ruby-webrick (1.8.1-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libjson-perl (4.10000-1) ... Setting up fonts-liberation (1:2.1.5-3) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up openssl (3.3.2-1) ... Setting up readline-common (8.2-5) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libjs-sphinxdoc (7.4.7-3) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up sphinx-common (7.4.7-3) ... Setting up libnsl2:amd64 (1.3.0-3+b2) ... Setting up libpython3.12-stdlib:amd64 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up debhelper (13.20) ... Setting up dh-exec (0.30) ... Setting up libpython3.12t64:amd64 (3.12.6-1) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up libpython3.12-dev:amd64 (3.12.6-1) ... Setting up python3-zipp (3.20.2-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b1) ... Setting up python3-roman (4.2-1) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.1-1) ... Setting up python3-certifi (2024.8.30-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up python3-idna (3.8-2) ... Setting up python3.12-dev (3.12.6-1) ... Setting up cython3 (3.0.11+dfsg-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-urllib3 (2.0.7-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-more-itertools (10.4.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up libpython3-dev:amd64 (3.12.6-1) ... Setting up python3-jaraco.functools (4.0.2-1) ... Setting up python3-screed (1.1.3-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-charset-normalizer (3.3.2-4) ... Setting up python3-pytest (8.3.3-1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-all (3.12.6-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up libpython3-all-dev:amd64 (3.12.6-1) ... Setting up python3-dev (3.12.6-1) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-all-dev (3.12.6-1) ... Setting up python3-setuptools (74.1.2-2) ... Setting up python3-babel (2.14.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-pytest-runner (2.11.1-4) ... Setting up dh-python (6.20240824) ... Setting up rake (13.2.1-1) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b4) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up libruby3.1t64:amd64 (3.1.2-8.4) ... Setting up ruby3.1 (3.1.2-8.4) ... Setting up libruby:amd64 (1:3.1+nmu1) ... Setting up ruby (1:3.1+nmu1) ... Setting up ruby-asciidoctor (2.0.23-1) ... Setting up asciidoctor (2.0.23-1) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (7.4.7-3) ... Setting up python3-guzzle-sphinx-theme (0.7.11-6) ... Setting up python3-sphinxcontrib.autoprogram (0.1.9-1) ... Processing triggers for ca-certificates (20240203) ... 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/reproducible-path/khmer-3.0.0~a3+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_3.0.0~a3+dfsg-8_source.changes dpkg-buildpackage: info: source package khmer dpkg-buildpackage: info: source version 3.0.0~a3+dfsg-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg' dh_auto_clean || /bin/true pybuild --clean -i python{version} -p 3.12 I: pybuild base:311: python3.12 setup.py clean /build/reproducible-path/khmer-3.0.0~a3+dfsg/versioneer.py:421: SyntaxWarning: invalid escape sequence '\s' LONG_VERSION_PY['git'] = ''' *** NOTE: Found Cython, extension files will be transpiled if this is an install invocation. /usr/lib/python3/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) /usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) /usr/lib/python3/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running clean removing '/build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.12' 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/reproducible-path/khmer-3.0.0~a3+dfsg/src/oxli' (cd ../../third-party/cqf && make clean) make[3]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' rm -f *.o gqf.o make[3]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' rm -f *.o *.a *.so* oxli.pc make[2]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/src/oxli' rm -rf __pycache__ .eggs make[1]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/khmer-common.substvars debian/khmer.substvars debian/liboxli1.substvars debian/liboxli-dev.substvars ./khmer/_oxli/assembly.cpp ./khmer/_oxli/graphs.cpp ./khmer/_oxli/hashing.cpp ./khmer/_oxli/hashset.cpp ./khmer/_oxli/hllcounter.cpp ./khmer/_oxli/labeling.cpp ./khmer/_oxli/legacy_partitioning.cpp ./khmer/_oxli/parsing.cpp ./khmer/_oxli/readaligner.cpp ./khmer/_oxli/traversal.cpp ./khmer/_oxli/utils.cpp debian/files rm -fr -- debian/khmer-common/ debian/tmp/ debian/khmer/ debian/liboxli1/ debian/liboxli-dev/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --with sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild pybuild --configure -i python{version} -p 3.12 I: pybuild base:311: python3.12 setup.py config /build/reproducible-path/khmer-3.0.0~a3+dfsg/versioneer.py:421: SyntaxWarning: invalid escape sequence '\s' LONG_VERSION_PY['git'] = ''' *** NOTE: Found Cython, extension files will be transpiled if this is an install invocation. /usr/lib/python3/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) /usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) /usr/lib/python3/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg' dh_auto_build pybuild --build -i python{version} -p 3.12 I: pybuild base:311: /usr/bin/python3 setup.py build *** NOTE: Found Cython, extension files will be transpiled if this is an install invocation. /usr/lib/python3/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) /usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) /usr/lib/python3/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running build running build_py creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer copying khmer/kfile.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer copying khmer/khmer_logger.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer copying khmer/khmer_args.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer copying khmer/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer copying khmer/trimming.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer copying khmer/utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer copying khmer/_version.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer copying khmer/thread_utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_lump.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_memory.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_oxli_functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_qfstorage.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_nibblestorage.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_subset_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_version.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_read_handling.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_sequence_validation.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_script_output.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_read_parsers.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_sandbox_scripts.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_normalize_by_median.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_scripts.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_hashset.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_banding.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_counttable.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_script_arguments.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/graph_features.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_cython_parsing.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_threaded_sequence_processor.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_hll.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_counting_single.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_countgraph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_tabletype.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_labelhash.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_cpython_hierarchy.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_read_aligner.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_filter_abund.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/khmer_tst_utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_assembly.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_nodegraph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/table_fixtures.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests copying tests/test_streaming_io.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli copying oxli/build_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli copying oxli/partition.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli copying oxli/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli copying oxli/functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_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' dependency include/oxli/khmer.hh won't be automatically included in the manifest: the path doesn't exist reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.cpp' under directory 'khmer/_oxli' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'khmer.egg-info/SOURCES.txt' copying tests/.gitignore -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.truncated.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.truncated.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/README.rst -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/all-A.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k12.ct -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k12.ht -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k32.stoptags -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k32.tagset -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/banding-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/biglump-random-20-a.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/bogus.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/branched-genome.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/casava_18-pe.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/combine_parts_1.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-all-paired-all-keep.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-none-paired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-some-paired-all-keep.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/fakelump.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/fakelump.fa.stoptags.txt -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/filter-test-A.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/filter-test-B.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k12.ht -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k12.ht.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k32.stoptags -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k32.tagset -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/multi-output.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/normC20k20.ct -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/old-style-format-w-comments.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.badleft -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.badright -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.paired_bad -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken2.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken2.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken3.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken3.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken4.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken4.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-2.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-broken.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-witherror.fa.pe -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa.pe -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa.se -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq.pe -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq.se -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired.malformat.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired.malformat.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/paired_one.base.dif.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-X2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.even.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.part -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.odd.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-b.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/random-31-c.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/readaligner-default.json -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/readaligner-k12.json -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/real-partition-small.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/real-partition-tiny.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/seq-a.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/seq-b.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/simple-genome-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/simple-genome.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/single-read.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/single-read.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.paired.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.paired2.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-3.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-impaired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-paired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-paired.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-empty.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-empty.fa.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-error-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-n-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-filter-abund-Ns.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph5.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-labels.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-large.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-multi.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-output-partitions.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-overlap1.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-overlap2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fq.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fq.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-short.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-contigs.fp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/test-transcript.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/truncated.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/unclean-reads.fastq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying tests/test-data/valid-read-testing.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data copying khmer/_oxli/assembly.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/assembly.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/hashset.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/hashset.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/hllcounter.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/hllcounter.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/labeling.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/labeling.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/legacy_partitioning.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/legacy_partitioning.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/oxli_exception_convert.cc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/oxli_exception_convert.hh -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/oxli_types.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/readaligner.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/readaligner.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/traversal.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/traversal.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/utils.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/utils.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli UPDATING /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_version.py set /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_version.py to '3.0.0a3' running build_ext bash -c "cd third-party/cqf && make" make[2]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' g++ -std=c++11 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Ofast -I. -Wno-unused-result -Wno-strict-aliasing -Wno-unused-function gqf.c -c -o gqf.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ make[2]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' building 'khmer._khmer' extension creating build creating build/temp.linux-x86_64-cpython-312 creating build/temp.linux-x86_64-cpython-312/src creating build/temp.linux-x86_64-cpython-312/src/khmer creating build/temp.linux-x86_64-cpython-312/src/oxli creating build/temp.linux-x86_64-cpython-312/third-party creating build/temp.linux-x86_64-cpython-312/third-party/smhasher x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o -O3 -std=c++11 -fopenmp In file included from third-party/seqan/core/include/seqan/basic.h:62, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:40: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/modifier.h:66, from third-party/seqan/core/include/seqan/file.h:48, from third-party/seqan/core/include/seqan/stream.h:70, from third-party/seqan/core/include/seqan/seq_io.h:45: third-party/seqan/core/include/seqan/modifier/modifier_functors.h:68:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 68 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from src/oxli/read_parsers.cc:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:91:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 91 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:115:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 115 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:169:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 169 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:178:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 178 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:188:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 188 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:198:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 198 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:208:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 208 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:217:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 217 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:229:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/file.h:117: third-party/seqan/core/include/seqan/file/string_external.h:1316:51: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1316 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/graph_algorithms.h:46, from third-party/seqan/core/include/seqan/graph_align.h:47, from third-party/seqan/core/include/seqan/align.h:54, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83: third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:340:23: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 340 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/graph_algorithms.h:47: third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm.h:643:23: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 643 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:79: third-party/seqan/core/include/seqan/align/gap_anchor.h:246:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/align/gap_anchor.h:256:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:59: third-party/seqan/core/include/seqan/store/store_align.h:322:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 322 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:332:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 332 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:342:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 342 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:352:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:362:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:372:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/storage.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/subset.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_khmer.cpython-312-x86_64-linux-gnu.so -fopenmp Compiling khmer/_oxli/hashing.pyx because it changed. [1/1] Cythonizing khmer/_oxli/hashing.pyx building 'khmer._oxli.hashing' extension creating build/temp.linux-x86_64-cpython-312/khmer creating build/temp.linux-x86_64-cpython-312/khmer/_oxli x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/hashing.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/hashing.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/hashing.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hashing.cpython-312-x86_64-linux-gnu.so -fopenmp warning: khmer/_oxli/parsing.pxd:60:20: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:61:31: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:78:21: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:79:32: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. Compiling khmer/_oxli/assembly.pyx because it changed. [1/1] Cythonizing khmer/_oxli/assembly.pyx building 'khmer._oxli.assembly' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/assembly.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/assembly.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:1334: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/assembly.cpp:1206:11: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/assembly.cpp:1215:11: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/assembly.cpp:1212:11: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/assembly.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/assembly.cpython-312-x86_64-linux-gnu.so -fopenmp warning: khmer/_oxli/parsing.pxd:60:20: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:61:31: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:78:21: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:79:32: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. Compiling khmer/_oxli/legacy_partitioning.pyx because it changed. [1/1] Cythonizing khmer/_oxli/legacy_partitioning.pyx building 'khmer._oxli.legacy_partitioning' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/legacy_partitioning.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/legacy_partitioning.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/legacy_partitioning.cpp:1333: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/legacy_partitioning.cpp:1205:11: note: this is the location of the previous definition 1205 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/legacy_partitioning.cpp:1214:11: note: this is the location of the previous definition 1214 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/legacy_partitioning.cpp:1211:11: note: this is the location of the previous definition 1211 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/legacy_partitioning.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/legacy_partitioning.cpython-312-x86_64-linux-gnu.so -fopenmp Compiling khmer/_oxli/hashset.pyx because it changed. [1/1] Cythonizing khmer/_oxli/hashset.pyx building 'khmer._oxli.hashset' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/hashset.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/hashset.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/hashset.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hashset.cpython-312-x86_64-linux-gnu.so -fopenmp warning: khmer/_oxli/parsing.pxd:60:20: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:61:31: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:78:21: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:79:32: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. Compiling khmer/_oxli/parsing.pyx because it changed. [1/1] Cythonizing khmer/_oxli/parsing.pyx building 'khmer._oxli.parsing' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/parsing.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/parsing.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/parsing.cpp:1321: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/parsing.cpp:1199:11: note: this is the location of the previous definition 1199 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/parsing.cpp:1208:11: note: this is the location of the previous definition 1208 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:1205:11: note: this is the location of the previous definition 1205 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/parsing.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/parsing.cpython-312-x86_64-linux-gnu.so -fopenmp Compiling khmer/_oxli/utils.pyx because it changed. [1/1] Cythonizing khmer/_oxli/utils.pyx building 'khmer._oxli.utils' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/utils.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/utils.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/utils.cpython-312-x86_64-linux-gnu.so -fopenmp warning: khmer/_oxli/parsing.pxd:60:20: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:61:31: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:78:21: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:79:32: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. Compiling khmer/_oxli/labeling.pyx because it changed. [1/1] Cythonizing khmer/_oxli/labeling.pyx building 'khmer._oxli.labeling' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/labeling.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/labeling.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/labeling.cpp:1333: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/labeling.cpp:1205:11: note: this is the location of the previous definition 1205 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/labeling.cpp:1214:11: note: this is the location of the previous definition 1214 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/labeling.cpp:1211:11: note: this is the location of the previous definition 1211 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/labeling.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/labeling.cpython-312-x86_64-linux-gnu.so -fopenmp warning: khmer/_oxli/parsing.pxd:60:20: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:61:31: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:78:21: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:79:32: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. Compiling khmer/_oxli/readaligner.pyx because it changed. [1/1] Cythonizing khmer/_oxli/readaligner.pyx building 'khmer._oxli.readaligner' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/readaligner.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/readaligner.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/readaligner.cpp:1334: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/readaligner.cpp:1206:11: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/readaligner.cpp:1215:11: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/readaligner.cpp:1212:11: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/readaligner.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/readaligner.cpython-312-x86_64-linux-gnu.so -fopenmp warning: khmer/_oxli/parsing.pxd:60:20: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:61:31: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:78:21: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:79:32: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. Compiling khmer/_oxli/graphs.pyx because it changed. [1/1] Cythonizing khmer/_oxli/graphs.pyx building 'khmer._oxli.graphs' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/graphs.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/graphs.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:1334: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/graphs.cpp:1206:11: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/graphs.cpp:1215:11: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/graphs.cpp:1212:11: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/graphs.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/graphs.cpython-312-x86_64-linux-gnu.so -fopenmp warning: khmer/_oxli/parsing.pxd:60:20: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:61:31: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:78:21: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:79:32: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. Compiling khmer/_oxli/traversal.pyx because it changed. [1/1] Cythonizing khmer/_oxli/traversal.pyx building 'khmer._oxli.traversal' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/traversal.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/traversal.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/traversal.cpp:1334: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/traversal.cpp:1206:11: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/traversal.cpp:1215:11: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/traversal.cpp:1212:11: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/traversal.cpython-312-x86_64-linux-gnu.so -fopenmp warning: khmer/_oxli/parsing.pxd:60:20: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:61:31: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:78:21: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:79:32: Rvalue-reference as function argument not supported warning: khmer/_oxli/parsing.pxd:173:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:175:34: Declarations should not be declared inline. Compiling khmer/_oxli/hllcounter.pyx because it changed. [1/1] Cythonizing khmer/_oxli/hllcounter.pyx building 'khmer._oxli.hllcounter' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/hllcounter.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/hllcounter.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/hllcounter.cpp:1327: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/hllcounter.cpp:1201:11: note: this is the location of the previous definition 1201 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/hllcounter.cpp:1210:11: note: this is the location of the previous definition 1210 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/hllcounter.cpp:1207:11: note: this is the location of the previous definition 1207 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hllcounter.cpython-312-x86_64-linux-gnu.so -fopenmp running build_scripts creating build/scripts-3.12 copying and adjusting scripts/unique-kmers.py -> build/scripts-3.12 copying and adjusting scripts/count-median.py -> build/scripts-3.12 copying and adjusting scripts/load-into-counting.py -> build/scripts-3.12 copying and adjusting scripts/normalize-by-median.py -> build/scripts-3.12 copying and adjusting scripts/make-initial-stoptags.py -> build/scripts-3.12 copying and adjusting scripts/extract-paired-reads.py -> build/scripts-3.12 copying and adjusting scripts/sample-reads-randomly.py -> build/scripts-3.12 copying and adjusting scripts/abundance-dist.py -> build/scripts-3.12 copying and adjusting scripts/partition-graph.py -> build/scripts-3.12 copying and adjusting scripts/extract-partitions.py -> build/scripts-3.12 copying and adjusting scripts/filter-abund.py -> build/scripts-3.12 copying and adjusting scripts/readstats.py -> build/scripts-3.12 copying and adjusting scripts/trim-low-abund.py -> build/scripts-3.12 copying and adjusting scripts/merge-partitions.py -> build/scripts-3.12 copying and adjusting scripts/abundance-dist-single.py -> build/scripts-3.12 copying and adjusting scripts/interleave-reads.py -> build/scripts-3.12 copying and adjusting scripts/find-knots.py -> build/scripts-3.12 copying and adjusting scripts/fastq-to-fasta.py -> build/scripts-3.12 copying and adjusting scripts/load-graph.py -> build/scripts-3.12 copying and adjusting scripts/extract-long-sequences.py -> build/scripts-3.12 copying and adjusting scripts/split-paired-reads.py -> build/scripts-3.12 copying and adjusting scripts/do-partition.py -> build/scripts-3.12 copying and adjusting scripts/annotate-partitions.py -> build/scripts-3.12 copying and adjusting scripts/filter-stoptags.py -> build/scripts-3.12 copying and adjusting scripts/filter-abund-single.py -> build/scripts-3.12 changing mode of build/scripts-3.12/unique-kmers.py from 644 to 755 changing mode of build/scripts-3.12/count-median.py from 644 to 755 changing mode of build/scripts-3.12/load-into-counting.py from 644 to 755 changing mode of build/scripts-3.12/normalize-by-median.py from 644 to 755 changing mode of build/scripts-3.12/make-initial-stoptags.py from 644 to 755 changing mode of build/scripts-3.12/extract-paired-reads.py from 644 to 755 changing mode of build/scripts-3.12/sample-reads-randomly.py from 644 to 755 changing mode of build/scripts-3.12/abundance-dist.py from 644 to 755 changing mode of build/scripts-3.12/partition-graph.py from 644 to 755 changing mode of build/scripts-3.12/extract-partitions.py from 644 to 755 changing mode of build/scripts-3.12/filter-abund.py from 644 to 755 changing mode of build/scripts-3.12/readstats.py from 644 to 755 changing mode of build/scripts-3.12/trim-low-abund.py from 644 to 755 changing mode of build/scripts-3.12/merge-partitions.py from 644 to 755 changing mode of build/scripts-3.12/abundance-dist-single.py from 644 to 755 changing mode of build/scripts-3.12/interleave-reads.py from 644 to 755 changing mode of build/scripts-3.12/find-knots.py from 644 to 755 changing mode of build/scripts-3.12/fastq-to-fasta.py from 644 to 755 changing mode of build/scripts-3.12/load-graph.py from 644 to 755 changing mode of build/scripts-3.12/extract-long-sequences.py from 644 to 755 changing mode of build/scripts-3.12/split-paired-reads.py from 644 to 755 changing mode of build/scripts-3.12/do-partition.py from 644 to 755 changing mode of build/scripts-3.12/annotate-partitions.py from 644 to 755 changing mode of build/scripts-3.12/filter-stoptags.py from 644 to 755 changing mode of build/scripts-3.12/filter-abund-single.py from 644 to 755 ln -sf `pybuild --print build_dir|awk -F: '{print $2}'`/khmer/*.so khmer && \ ./setup.py develop --user && sphinx-build doc build/sphinx/html *** NOTE: Found Cython, extension files will be transpiled if this is an install invocation. /usr/lib/python3/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) /usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) /usr/lib/python3/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running develop /usr/lib/python3/dist-packages/setuptools/command/develop.py:41: EasyInstallDeprecationWarning: easy_install command is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` and ``easy_install``. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://github.com/pypa/setuptools/issues/917 for details. ******************************************************************************** !! easy_install.initialize_options(self) /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() 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 dependency include/oxli/khmer.hh won't be automatically included in the manifest: the path doesn't exist reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'khmer.egg-info/SOURCES.txt' running build_ext bash -c "cd third-party/cqf && make" make[2]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' building 'khmer._khmer' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o -O3 -std=c++11 -fopenmp In file included from third-party/seqan/core/include/seqan/basic.h:62, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:40: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/modifier.h:66, from third-party/seqan/core/include/seqan/file.h:48, from third-party/seqan/core/include/seqan/stream.h:70, from third-party/seqan/core/include/seqan/seq_io.h:45: third-party/seqan/core/include/seqan/modifier/modifier_functors.h:68:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 68 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from src/oxli/read_parsers.cc:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:91:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 91 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:115:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 115 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:169:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 169 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:178:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 178 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:188:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 188 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:198:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 198 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:208:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 208 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:217:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 217 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:229:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/file.h:117: third-party/seqan/core/include/seqan/file/string_external.h:1316:51: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1316 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/graph_algorithms.h:46, from third-party/seqan/core/include/seqan/graph_align.h:47, from third-party/seqan/core/include/seqan/align.h:54, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83: third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:340:23: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 340 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/graph_algorithms.h:47: third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm.h:643:23: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 643 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:79: third-party/seqan/core/include/seqan/align/gap_anchor.h:246:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/align/gap_anchor.h:256:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:59: third-party/seqan/core/include/seqan/store/store_align.h:322:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 322 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:332:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 332 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:342:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 342 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:352:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:362:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:372:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/storage.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/subset.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -fopenmp creating build/lib.linux-x86_64-cpython-312 creating build/lib.linux-x86_64-cpython-312/khmer x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_khmer.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hashing' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/hashing.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/hashing.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp creating build/lib.linux-x86_64-cpython-312/khmer/_oxli x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/hashing.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/hashing.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.assembly' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/assembly.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/assembly.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:1334: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/assembly.cpp:1206:11: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/assembly.cpp:1215:11: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/assembly.cpp:1212:11: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/assembly.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/assembly.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.legacy_partitioning' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/legacy_partitioning.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/legacy_partitioning.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/legacy_partitioning.cpp:1333: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/legacy_partitioning.cpp:1205:11: note: this is the location of the previous definition 1205 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/legacy_partitioning.cpp:1214:11: note: this is the location of the previous definition 1214 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/legacy_partitioning.cpp:1211:11: note: this is the location of the previous definition 1211 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/legacy_partitioning.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/legacy_partitioning.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hashset' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/hashset.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/hashset.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/hashset.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/hashset.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.parsing' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/parsing.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/parsing.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/parsing.cpp:1321: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/parsing.cpp:1199:11: note: this is the location of the previous definition 1199 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/parsing.cpp:1208:11: note: this is the location of the previous definition 1208 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:1205:11: note: this is the location of the previous definition 1205 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/parsing.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/parsing.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.utils' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/utils.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/utils.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/utils.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.labeling' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/labeling.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/labeling.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/labeling.cpp:1333: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/labeling.cpp:1205:11: note: this is the location of the previous definition 1205 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/labeling.cpp:1214:11: note: this is the location of the previous definition 1214 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/labeling.cpp:1211:11: note: this is the location of the previous definition 1211 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/labeling.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/labeling.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.readaligner' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/readaligner.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/readaligner.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/readaligner.cpp:1334: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/readaligner.cpp:1206:11: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/readaligner.cpp:1215:11: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/readaligner.cpp:1212:11: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/readaligner.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/readaligner.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.graphs' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/graphs.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/graphs.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:1334: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/graphs.cpp:1206:11: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/graphs.cpp:1215:11: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/graphs.cpp:1212:11: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/graphs.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/graphs.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.traversal' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/traversal.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/traversal.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/traversal.cpp:1334: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/traversal.cpp:1206:11: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/traversal.cpp:1215:11: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/traversal.cpp:1212:11: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/traversal.cpython-312-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hllcounter' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/hllcounter.cpp -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/hllcounter.o -O3 -std=c++11 -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/hllcounter.cpp:1327: include/khmer/_cpy_utils.hh:17:9: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | ^~~~~~~~~~~ khmer/_oxli/hllcounter.cpp:1201:11: note: this is the location of the previous definition 1201 | #define PyInt_Check(op) PyLong_Check(op) | ^~~~~~~~~~~ include/khmer/_cpy_utils.hh:18:9: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | ^~~~~~~~~~~~ khmer/_oxli/hllcounter.cpp:1210:11: note: this is the location of the previous definition 1210 | #define PyInt_AsLong PyLong_AsLong | ^~~~~~~~~~~~ include/khmer/_cpy_utils.hh:19:9: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | ^~~~~~~~~~~~~~ khmer/_oxli/hllcounter.cpp:1207:11: note: this is the location of the previous definition 1207 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/khmer/_oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-312/khmer/_oxli/hllcounter.cpython-312-x86_64-linux-gnu.so -fopenmp copying build/lib.linux-x86_64-cpython-312/khmer/_khmer.cpython-312-x86_64-linux-gnu.so -> khmer copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/hashing.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/assembly.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/legacy_partitioning.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/hashset.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/parsing.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/utils.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/labeling.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/readaligner.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/graphs.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/traversal.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-312/khmer/_oxli/hllcounter.cpython-312-x86_64-linux-gnu.so -> khmer/_oxli Creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/lib/python3.12/site-packages/khmer.egg-link (link to .) Adding khmer 3.0.0a3 to easy-install.pth file Installing unique-kmers.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing count-median.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing load-into-counting.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing normalize-by-median.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing make-initial-stoptags.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing extract-paired-reads.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing sample-reads-randomly.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing abundance-dist.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing partition-graph.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing extract-partitions.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing filter-abund.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing readstats.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing trim-low-abund.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing merge-partitions.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing abundance-dist-single.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing interleave-reads.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing find-knots.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing fastq-to-fasta.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing load-graph.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing extract-long-sequences.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing split-paired-reads.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing do-partition.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing annotate-partitions.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing filter-stoptags.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installing filter-abund-single.py script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Installed /build/reproducible-path/khmer-3.0.0~a3+dfsg Processing dependencies for khmer==3.0.0a3 Searching for screed==1.1.3 Best match: screed 1.1.3 Adding screed 1.1.3 to easy-install.pth file Installing screed script to /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/bin Using /usr/lib/python3/dist-packages Finished processing dependencies for khmer==3.0.0a3 Running Sphinx v7.4.7 loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 41 source files that are out of date updating environment: [new config] 41 added, 0 changed, 0 removed reading sources... 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[100%] user/scripts looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/khmer-3.0.0~a3+dfsg/doc/dev/hackathon.rst: WARNING: document isn't included in any toctree /build/reproducible-path/khmer-3.0.0~a3+dfsg/doc/dev/python-api.rst: WARNING: document isn't included in any toctree done preparing documents... done copying assets... copying static files... done copying extra files... done copying assets: done writing output... [ 2%] LICENSE writing output... [ 5%] citations writing output... [ 7%] contributors writing output... [ 10%] dev/CODE_OF_CONDUCT writing output... [ 12%] dev/a-quick-guide-to-testing writing output... [ 15%] dev/binary-file-formats writing output... [ 17%] dev/codebase-guide writing output... [ 20%] dev/development writing output... [ 22%] dev/for-khmer-developers writing output... [ 24%] dev/getting-started writing output... [ 27%] dev/guidelines-continued-dev writing output... 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[100%] user/scripts /build/reproducible-path/khmer-3.0.0~a3+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: 'load-into-counting.py -N' /build/reproducible-path/khmer-3.0.0~a3+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: 'load-into-counting.py --n_tables' /build/reproducible-path/khmer-3.0.0~a3+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: 'load-into-counting.py -x' /build/reproducible-path/khmer-3.0.0~a3+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: 'load-into-counting.py --max-tablesize' /build/reproducible-path/khmer-3.0.0~a3+dfsg/doc/user/scripts.rst:79: WARNING: unknown option: '-x' /build/reproducible-path/khmer-3.0.0~a3+dfsg/doc/user/scripts.rst:79: WARNING: unknown option: '-N' /build/reproducible-path/khmer-3.0.0~a3+dfsg/doc/user/scripts.rst:87: WARNING: unknown option: '-x' /build/reproducible-path/khmer-3.0.0~a3+dfsg/doc/user/scripts.rst:87: WARNING: unknown option: '-N' generating indices... genindex done writing additional pages... search done copying images... 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The HTML pages are in build/sphinx/html. asciidoctor --backend manpage -a reproducible debian/khmer.1.adoc /usr/bin/make -C src/oxli clean make[2]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/src/oxli' (cd ../../third-party/cqf && make clean) make[3]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' rm -f *.o gqf.o make[3]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' rm -f *.o *.a *.so* oxli.pc make[2]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/src/oxli' /usr/bin/make -C src/oxli all USE_SYSTEM_ZLIB="true" USE_SYSTEM_LIBBZ2="true" make[2]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/src/oxli' (cd ../../third-party/cqf && make) make[3]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' g++ -std=c++11 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wshadow -Wcast-align -Wstrict-prototypes -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -fopenmp -DNO_UNIQUE_RC=0 -Wall -Ofast -I. -Wno-unused-result -Wno-strict-aliasing -Wno-unused-function gqf.c -c -o gqf.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: command-line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ gqf.c: In function 'void remove_replace_slots_and_shift_remainders_and_runends_and_offsets(QF*, int, uint64_t, uint64_t, const uint64_t*, uint64_t, uint64_t)': gqf.c:789:34: warning: declaration of 'i' shadows a previous local [-Wshadow] 789 | uint64_t i; | ^ gqf.c:748:18: note: shadowed declaration is here 748 | uint64_t i; | ^ gqf.c:834:42: warning: declaration of 'i' shadows a previous local [-Wshadow] 834 | uint64_t i; | ^ gqf.c:748:18: note: shadowed declaration is here 748 | uint64_t i; | ^ make[3]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o hashtable.o hashtable.cc hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': hashtable.cc:626:1: required from here 626 | ); | ^ hashtable.cc:138:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 138 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': hashtable.cc:643:1: required from here 643 | ); | ^ hashtable.cc:208:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 208 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_with_mask(oxli::read_parsers::ReadParserPtr&, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': hashtable.cc:662:1: required from here 662 | ); | ^ hashtable.cc:168:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 168 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding_with_mask(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': hashtable.cc:685:1: required from here 685 | ); | ^ hashtable.cc:250:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 250 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from hashtable.cc:49: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o hashgraph.o hashgraph.cc In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from ../../include/oxli/hashgraph.hh:52, from hashgraph.cc:47: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o hllcounter.o hllcounter.cc hllcounter.cc: In instantiation of 'void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': hllcounter.cc:435:1: required from here 435 | ); | ^ hllcounter.cc:366:40: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 366 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from hllcounter.cc:48: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o kmer_hash.o kmer_hash.cc In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from kmer_hash.cc:49: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o labelhash.o labelhash.cc In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from ../../include/oxli/hashgraph.hh:52, from labelhash.cc:44: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o traversal.o traversal.cc In file included from traversal.cc:39: traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]': traversal.cc:202:5: required from here 202 | left_gatherer(ht, filters), | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ../../include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ ../../include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]': traversal.cc:203:5: required from here 203 | right_gatherer(ht, filters) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ ../../include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from traversal.cc:38: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o read_aligner.o read_aligner.cc In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from read_aligner.cc:46: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from read_aligner.cc:48: ../../include/oxli/read_aligner.hh:114:15: warning: 'oxli::freq_default' defined but not used [-Wunused-variable] 114 | static double freq_default[] = { log2(0.955), | ^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o read_parsers.o read_parsers.cc In file included from ../../third-party/seqan/core/include/seqan/basic.h:62, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:40: ../../third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from ../../third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/modifier.h:66, from ../../third-party/seqan/core/include/seqan/file.h:48, from ../../third-party/seqan/core/include/seqan/stream.h:70, from ../../third-party/seqan/core/include/seqan/seq_io.h:45: ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:68:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 68 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from read_parsers.cc:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:91:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 91 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:115:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 115 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:169:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 169 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:178:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 178 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:188:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 188 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:198:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 198 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:208:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 208 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:217:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 217 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/modifier/modifier_functors.h:229:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/file.h:117: ../../third-party/seqan/core/include/seqan/file/string_external.h:1316:51: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1316 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/graph_algorithms.h:46, from ../../third-party/seqan/core/include/seqan/graph_align.h:47, from ../../third-party/seqan/core/include/seqan/align.h:54, from ../../third-party/seqan/core/include/seqan/store.h:38, from ../../third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from ../../third-party/seqan/core/include/seqan/seq_io.h:83: ../../third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:340:23: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 340 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/graph_algorithms.h:47: ../../third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm.h:643:23: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 643 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/align.h:79: ../../third-party/seqan/core/include/seqan/align/gap_anchor.h:246:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/align/gap_anchor.h:256:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/align.h:116: ../../third-party/seqan/core/include/seqan/align/dp_cell_affine.h: In member function 'seqan::DPCell_ >& seqan::DPCell_ >::operator=(const seqan::DPCell_ >&)': ../../third-party/seqan/core/include/seqan/align/dp_cell_affine.h:84:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 84 | if (this != &other) | ^~ ../../third-party/seqan/core/include/seqan/align/dp_cell_affine.h:86:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 86 | _horizontalScore = other._horizontalScore; | ^~~~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/align.h:166: ../../third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function 'int seqan::_globalAlignmentScore(const String&, const String&, const MyersBitVector&)': ../../third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ ../../third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from ../../third-party/seqan/core/include/seqan/align.h:174: ../../third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function 'seqan::Pair > seqan::_alignBandedSmithWatermanTrace(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)': ../../third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ ../../third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from ../../third-party/seqan/core/include/seqan/bam_io.h:107, from ../../third-party/seqan/core/include/seqan/store.h:41: ../../third-party/seqan/core/include/seqan/bam_io/bam_stream.h: At global scope: ../../third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../../third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/store.h:59: ../../third-party/seqan/core/include/seqan/store/store_align.h:322:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 322 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/store/store_align.h:332:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 332 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/store/store_align.h:342:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 342 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/store/store_align.h:352:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/store/store_align.h:362:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../third-party/seqan/core/include/seqan/store/store_align.h:372:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/store.h:61: ../../third-party/seqan/core/include/seqan/store/store_all.h: In function 'void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)': ../../third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 1733 | if (alignQualityStoreLengthPre == 0u) | ^~ ../../third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o subset.o subset.cc subset.cc: In member function 'size_t oxli::SubsetPartition::output_partitioned_file(const std::string&, const std::string&, bool, oxli::CallbackFn, void*)': subset.cc:136:24: warning: unused variable 'ksize' [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from ../../include/oxli/hashgraph.hh:52, from subset.cc:47: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o kmer_filters.o kmer_filters.cc In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from kmer_filters.cc:40: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o assembler.o assembler.cc In file included from assembler.cc:38: ../../include/oxli/assembler.hh: In constructor 'oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)': ../../include/oxli/assembler.hh:80:23: warning: 'oxli::LinearAssembler::graph' will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ ../../include/oxli/assembler.hh:79:16: warning: 'oxli::WordLength oxli::LinearAssembler::_ksize' [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ assembler.cc: In destructor 'oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()': assembler.cc:189:5: warning: deleting object of polymorphic class type 'oxli::LinearAssembler' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ ../../include/oxli/assembler.hh: In constructor 'oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)': ../../include/oxli/assembler.hh:158:16: warning: 'oxli::JunctionCountAssembler::_ksize' will be initialized after [-Wreorder] 158 | WordLength _ksize; | ^~~~~~ ../../include/oxli/assembler.hh:153:15: warning: 'oxli::Traverser oxli::JunctionCountAssembler::traverser' [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ ../../include/oxli/assembler.hh:153:15: warning: 'oxli::JunctionCountAssembler::traverser' will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ ../../include/oxli/assembler.hh:151:21: warning: 'oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm' [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/assembler.hh:43: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o alphabets.o alphabets.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -c -o murmur3.o ../../third-party/smhasher/MurmurHash3.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o storage.o storage.cc In file included from /usr/include/c++/14/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from storage.cc:44: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' 30 | hasher(maskfnc(wordsize)), | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ../../include/oxli/kmer_hash.hh:434:30: required from here 434 | _initialized(false), fwd_hasher(k), bwd_hasher(k) | ^~~~~~~~~~~~~ ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fPIC -fno-omit-frame-pointer -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -I ../../third-party/cqf/ -I ../../third-party/rollinghash -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -fno-omit-frame-pointer -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -Wl,-soname=liboxli.so.1 -shared -o liboxli.so.1 hashtable.o hashgraph.o hllcounter.o kmer_hash.o labelhash.o traversal.o read_aligner.o read_parsers.o subset.o kmer_filters.o assembler.o alphabets.o murmur3.o storage.o ../../third-party/cqf/gqf.o ln -sf liboxli.so.1 liboxli.so ar rcs liboxli.a hashtable.o hashgraph.o hllcounter.o kmer_hash.o labelhash.o traversal.o read_aligner.o read_parsers.o subset.o kmer_filters.o assembler.o alphabets.o murmur3.o storage.o ../../third-party/cqf/gqf.o ranlib liboxli.a sed -e 's,@prefix@,/usr/local,' -e 's,@VERSION@,,' oxli.pc.in >oxli.pc make[2]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/src/oxli' make[1]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg' rm -f debian/khmer-common.debhelper.log debian/khmer.debhelper.log debian/liboxli-dev.debhelper.log debian/liboxli1.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg' dh_auto_install install -m0755 -d /build/reproducible-path/khmer-3.0.0\~a3\+dfsg/debian/tmp pybuild --install -i python{version} -p 3.12 --dest-dir /build/reproducible-path/khmer-3.0.0\~a3\+dfsg/debian/tmp I: pybuild base:311: /usr/bin/python3 setup.py install --root '/build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer' '--install-scripts=/usr/lib/khmer/bin' *** NOTE: Found Cython, extension files will be transpiled if this is an install invocation. /usr/lib/python3/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) /usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) /usr/lib/python3/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() 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 dependency include/oxli/khmer.hh won't be automatically included in the manifest: the path doesn't exist reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'khmer.egg-info/SOURCES.txt' copying khmer/_oxli/assembly.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/hashset.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/hllcounter.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/labeling.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/legacy_partitioning.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/readaligner.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/traversal.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli copying khmer/_oxli/utils.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli UPDATING /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_version.py set /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_version.py to '3.0.0a3' running build_ext bash -c "cd third-party/cqf && make" make[2]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' building 'khmer._khmer' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o -O3 -std=c++11 -fopenmp In file included from third-party/seqan/core/include/seqan/basic.h:62, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:40: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/modifier.h:66, from third-party/seqan/core/include/seqan/file.h:48, from third-party/seqan/core/include/seqan/stream.h:70, from third-party/seqan/core/include/seqan/seq_io.h:45: third-party/seqan/core/include/seqan/modifier/modifier_functors.h:68:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 68 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from src/oxli/read_parsers.cc:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:91:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 91 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:115:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 115 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:169:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 169 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:178:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 178 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:188:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 188 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:198:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 198 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:208:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 208 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:217:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 217 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/modifier/modifier_functors.h:229:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 229 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/file.h:117: third-party/seqan/core/include/seqan/file/string_external.h:1316:51: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1316 | struct testIODone : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/graph_algorithms.h:46, from third-party/seqan/core/include/seqan/graph_align.h:47, from third-party/seqan/core/include/seqan/align.h:54, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83: third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:340:23: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 340 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/graph_algorithms.h:47: third-party/seqan/core/include/seqan/graph_algorithms/graph_algorithm.h:643:23: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 643 | public ::std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:79: third-party/seqan/core/include/seqan/align/gap_anchor.h:246:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 246 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/align/gap_anchor.h:256:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 256 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:59: third-party/seqan/core/include/seqan/store/store_align.h:322:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 322 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:332:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 332 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:342:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 342 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:352:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:362:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ third-party/seqan/core/include/seqan/store/store_align.h:372:23: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public ::std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/storage.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/subset.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.12 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -fopenmp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/khmer-3.0.0~a3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-312/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-312/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-312/src/oxli/assembler.o build/temp.linux-x86_64-cpython-312/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-312/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-312/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-312/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-312/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-312/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-312/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-312/src/oxli/storage.o build/temp.linux-x86_64-cpython-312/src/oxli/subset.o build/temp.linux-x86_64-cpython-312/src/oxli/traversal.o build/temp.linux-x86_64-cpython-312/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_khmer.cpython-312-x86_64-linux-gnu.so -fopenmp running build_scripts running install_lib creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12 creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli/build_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli/partition.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli/functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/kfile.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/khmer_logger.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/khmer_args.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_lump.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_memory.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_oxli_functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_qfstorage.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_nibblestorage.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/.gitignore -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_subset_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_version.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_read_handling.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_sequence_validation.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_script_output.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_read_parsers.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_sandbox_scripts.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_normalize_by_median.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_scripts.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_hashset.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_banding.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_counttable.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_script_arguments.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/graph_features.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_cython_parsing.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_threaded_sequence_processor.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_hll.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_counting_single.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_countgraph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_tabletype.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_labelhash.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_cpython_hierarchy.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-output-partitions.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/100-reads.fq.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/old-style-format-w-comments.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/100-reads.fq.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/badversion-k12.ht -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-reads.fq.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-slash1.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-mixed.fq.pe -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/README.rst -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-error-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/simple-genome.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired.malformat.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-fastq-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read-impaired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired.fa.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/badversion-k32.tagset -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken4.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/filter-test-A.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-X2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read-2.paired2.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-short.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-sweep-contigs.fp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken3.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-mixed-witherror.fa.pe -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/empty-file.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken2.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/truncated.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-graph5.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-mixed.fa.se -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/normC20k20.ct -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-large.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired.fa.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/real-partition-small.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/simple-genome-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-mixed.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-mixed-2.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/dn-test-some-paired-all-keep.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-fastq-n-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/goodversion-k32.tagset -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-labels.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-slash1.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-a.even.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-overlap1.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/filter-test-B.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/banding-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken4.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-overlap2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-a.fa.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-empty.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/multi-output.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-sweep-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/bogus.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-a.odd.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/biglump-random-20-a.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/empty-file -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/badversion-k32.stoptags -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-mixed.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/fakelump.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/dn-test-all-paired-all-keep.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/all-A.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/single-read.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-sweep-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read-paired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read-3.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/empty-file.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/badversion-k12.ct -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/dn-test-none-paired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/seq-b.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-a.fq.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-a.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-reads.fq.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-31-c.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/casava_18-pe.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-mixed.fa.pe -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-filter-abund-Ns.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken.fq.paired_bad -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-empty.fa.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-graph.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-a.fa.part -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/unclean-reads.fastq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/real-partition-tiny.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-multi.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-a.fa.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/branched-genome.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read-2.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired_one.base.dif.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/goodversion-k12.ht -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-fastq-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-mixed-broken.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/seq-a.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-mixed.fq.se -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/readaligner-k12.json -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/readaligner-default.json -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-a.fq.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-b.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/random-20-a.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired.malformat.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/goodversion-k12.ht.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/single-read.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-graph2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/combine_parts_1.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read-paired.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/goodversion-k32.stoptags -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read-2.paired.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/fakelump.fa.stoptags.txt -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-transcript.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-slash1.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken2.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/valid-read-testing.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/test-abund-read-2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken.fq.badright -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken.fq.badleft -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken3.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test-data/paired-broken.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_read_aligner.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_filter_abund.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/khmer_tst_utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_assembly.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_nodegraph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/table_fixtures.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/tests/test_streaming_io.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_khmer.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/trimming.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hllcounter.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/legacy_partitioning.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/parsing.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/utils.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hllcounter.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/graphs.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/oxli_exception_convert.cc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/assembly.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hashing.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/assembly.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/legacy_partitioning.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/utils.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hashing.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hashing.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hashset.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/parsing.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/readaligner.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/utils.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hashing.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/parsing.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/assembly.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/assembly.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/oxli_exception_convert.hh -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/labeling.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/traversal.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hashset.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/graphs.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/traversal.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/oxli_types.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/readaligner.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/labeling.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/graphs.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/labeling.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/readaligner.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/traversal.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/labeling.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/graphs.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/traversal.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/utils.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hashset.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hashset.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/parsing.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hllcounter.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/hllcounter.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/readaligner.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/legacy_partitioning.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/legacy_partitioning.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_version.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/thread_utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli/build_graph.py to build_graph.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli/partition.py to partition.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli/functions.py to functions.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/kfile.py to kfile.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/khmer_logger.py to khmer_logger.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/khmer_args.py to khmer_args.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_lump.py to test_lump.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_memory.py to test_memory.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_oxli_functions.py to test_oxli_functions.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_qfstorage.py to test_qfstorage.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_nibblestorage.py to test_nibblestorage.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_subset_graph.py to test_subset_graph.cpython-312.pyc /usr/lib/python3.12/dist-packages/khmer/tests/test_subset_graph.py:61: SyntaxWarning: "is" with 'int' literal. Did you mean "=="? /usr/lib/python3.12/dist-packages/khmer/tests/test_subset_graph.py:82: SyntaxWarning: "is" with 'int' literal. Did you mean "=="? /usr/lib/python3.12/dist-packages/khmer/tests/test_subset_graph.py:278: SyntaxWarning: "is" with 'int' literal. Did you mean "=="? /usr/lib/python3.12/dist-packages/khmer/tests/test_subset_graph.py:476: SyntaxWarning: "is" with 'int' literal. Did you mean "=="? /usr/lib/python3.12/dist-packages/khmer/tests/test_subset_graph.py:509: SyntaxWarning: "is" with 'int' literal. Did you mean "=="? byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_functions.py to test_functions.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_version.py to test_version.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_read_handling.py to test_read_handling.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_sequence_validation.py to test_sequence_validation.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_script_output.py to test_script_output.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_read_parsers.py to test_read_parsers.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_sandbox_scripts.py to test_sandbox_scripts.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_normalize_by_median.py to test_normalize_by_median.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_scripts.py to test_scripts.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_hashset.py to test_hashset.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_banding.py to test_banding.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_counttable.py to test_counttable.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_script_arguments.py to test_script_arguments.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/graph_features.py to graph_features.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_cython_parsing.py to test_cython_parsing.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_threaded_sequence_processor.py to test_threaded_sequence_processor.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_hll.py to test_hll.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_counting_single.py to test_counting_single.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_countgraph.py to test_countgraph.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_tabletype.py to test_tabletype.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_labelhash.py to test_labelhash.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_cpython_hierarchy.py to test_cpython_hierarchy.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_read_aligner.py to test_read_aligner.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_filter_abund.py to test_filter_abund.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_graph.py to test_graph.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/khmer_tst_utils.py to khmer_tst_utils.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_assembly.py to test_assembly.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_nodegraph.py to test_nodegraph.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/table_fixtures.py to table_fixtures.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/tests/test_streaming_io.py to test_streaming_io.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/trimming.py to trimming.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/utils.py to utils.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_version.py to _version.cpython-312.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/thread_utils.py to thread_utils.cpython-312.pyc running install_egg_info Copying khmer.egg-info to /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer-3.0.0a3.egg-info Skipping SOURCES.txt running install_scripts creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/unique-kmers.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/count-median.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/load-into-counting.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/normalize-by-median.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/make-initial-stoptags.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/extract-paired-reads.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/sample-reads-randomly.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/abundance-dist.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/partition-graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/extract-partitions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/filter-abund.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/readstats.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/trim-low-abund.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/merge-partitions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/abundance-dist-single.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/interleave-reads.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/find-knots.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/fastq-to-fasta.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/load-graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/extract-long-sequences.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/split-paired-reads.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/do-partition.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/annotate-partitions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/filter-stoptags.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.12/filter-abund-single.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/unique-kmers.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/count-median.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/load-into-counting.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/normalize-by-median.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/make-initial-stoptags.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/extract-paired-reads.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/sample-reads-randomly.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/abundance-dist.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/partition-graph.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/extract-partitions.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/filter-abund.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/readstats.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/trim-low-abund.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/merge-partitions.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/abundance-dist-single.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/interleave-reads.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/find-knots.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/fastq-to-fasta.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/load-graph.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/extract-long-sequences.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/split-paired-reads.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/do-partition.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/annotate-partitions.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/filter-stoptags.py to 755 changing mode of /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin/filter-abund-single.py to 755 PYBUILD_SYSTEM=custom \ PYBUILD_TEST_ARGS="cd {dir}; export PATH={destdir}/usr/lib/khmer/bin:$PATH ; \ cd {build_dir}; export PYTHONPATH=$(pwd); {interpreter} -m pytest \ -m 'not known_failing and not jenkins and not huge and not noroot'\ -q" dh_auto_test pybuild --test --test-pytest -i python{version} -p 3.12 I: pybuild base:311: cd '/build/reproducible-path/khmer-3.0.0~a3+dfsg'; export PATH='/build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer'/usr/lib/khmer/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games ; cd '/build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build'; export PYTHONPATH=/build/reproducible-path/khmer-3.0.0~a3+dfsg; python3.12 -m pytest -m 'not known_failing and not jenkins and not huge and not noroot' -q ============================= test session starts ============================== platform linux -- Python 3.12.6, pytest-8.3.3, pluggy-1.5.0 rootdir: /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build configfile: pytest.ini testpaths: tests plugins: typeguard-4.3.0 collected 1492 items / 47 deselected / 1445 selected tests/test_assembly.py ................................................. [ 3%] ........................................................................ [ 8%] ........................................................................ [ 13%] ..........................................X............................. [ 18%] ........................................................................ [ 23%] .................... [ 24%] tests/test_banding.py ............ [ 25%] tests/test_countgraph.py ........Fatal Python error: Aborted Current thread 0x00007f7fefc8e080 (most recent call first): File "/build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/tests/test_countgraph.py", line 212 in test_get_raw_tables_smallcountgraph File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159 in pytest_pyfunc_call File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627 in runtest File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174 in pytest_runtest_call File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242 in File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341 in from_call File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 241 in call_and_report File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 132 in runtestprotocol File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 113 in pytest_runtest_protocol File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ File "/usr/lib/python3/dist-packages/_pytest/main.py", line 362 in pytest_runtestloop File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ File "/usr/lib/python3/dist-packages/_pytest/main.py", line 337 in _main File "/usr/lib/python3/dist-packages/_pytest/main.py", line 283 in wrap_session File "/usr/lib/python3/dist-packages/_pytest/main.py", line 330 in pytest_cmdline_main File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 175 in main File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 201 in console_main File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 9 in File "", line 88 in _run_code File "", line 198 in _run_module_as_main Extension modules: khmer._khmer, khmer._oxli.hashing, khmer._oxli.utils, khmer._oxli.parsing, khmer._oxli.hashset, khmer._oxli.traversal, khmer._oxli.graphs, khmer._oxli.legacy_partitioning, khmer._oxli.labeling, khmer._oxli.assembly, khmer._oxli.readaligner, khmer._oxli.hllcounter (total: 12) Aborted E: pybuild pybuild:389: test: plugin custom failed with: exit code=134: cd '/build/reproducible-path/khmer-3.0.0~a3+dfsg'; export PATH='/build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer'/usr/lib/khmer/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games ; cd '/build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build'; export PYTHONPATH=/build/reproducible-path/khmer-3.0.0~a3+dfsg; python3.12 -m pytest -m 'not known_failing and not jenkins and not huge and not noroot' -q rm -fr -- /tmp/dh-xdg-rundir-mJozUTkN dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.12 returned exit code 13 make[1]: *** [debian/rules:29: override_dh_auto_test] Error 25 make[1]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg' make: *** [debian/rules:16: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/2070678 and its subdirectories khmer failed to build from source. removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/khmer_3.0.0~a3+dfsg-8.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/khmer_3.0.0~a3+dfsg-8.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/khmer_3.0.0~a3+dfsg-8.build1.log.gz' Sat Sep 28 13:34:50 UTC 2024 W: No second build log, what happened? Compressing the 1st log... b1/build.log: 91.7% -- replaced with stdout INSERT 0 1 INSERT 0 1 DELETE 1 [2024-09-28 13:34:51] INFO: Starting at 2024-09-28 13:34:51.285871 [2024-09-28 13:34:51] INFO: Generating the pages of 1 package(s) [2024-09-28 13:34:51] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/khmer didn't produce a buildlog, even though it has been built. [2024-09-28 13:34:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/khmer_3.0.0~a3+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/khmer_3.0.0~a3+dfsg-8.diff.gz is missing [2024-09-28 13:34:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/khmer_3.0.0~a3+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/khmer_3.0.0~a3+dfsg-8.diff.gz is missing [2024-09-28 13:34:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/khmer_3.0.0~a3+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/khmer_3.0.0~a3+dfsg-8.diff.gz is missing [2024-09-28 13:34:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/khmer_3.0.0~a3+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/khmer_3.0.0~a3+dfsg-8.diff.gz is missing [2024-09-28 13:34:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/khmer_3.0.0~a3+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/khmer_3.0.0~a3+dfsg-8.diff.gz is missing [2024-09-28 13:34:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/armhf/khmer_3.0.0~a3+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/armhf/khmer_3.0.0~a3+dfsg-8.diff.gz is missing [2024-09-28 13:34:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/khmer_3.0.0~a3+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/khmer_3.0.0~a3+dfsg-8.diff.gz is missing [2024-09-28 13:34:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/arm64/khmer_3.0.0~a3+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/arm64/khmer_3.0.0~a3+dfsg-4.diff.gz is missing [2024-09-28 13:34:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/khmer_3.0.0~a3+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/khmer_3.0.0~a3+dfsg-4.diff.gz is missing [2024-09-28 13:34:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/i386/khmer_3.0.0~a3+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/i386/khmer_3.0.0~a3+dfsg-4.diff.gz is missing [2024-09-28 13:34:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/armhf/khmer_2.1.2+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/armhf/khmer_2.1.2+dfsg-8.diff.gz is missing [2024-09-28 13:34:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/i386/khmer_2.1.2+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/i386/khmer_2.1.2+dfsg-8.diff.gz is missing [2024-09-28 13:34:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/experimental/amd64/khmer_3.0.0~a3+dfsg-9~0exp.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/experimental/amd64/khmer_3.0.0~a3+dfsg-9~0exp.diff.gz is missing [2024-09-28 13:34:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/experimental/arm64/khmer_3.0.0~a3+dfsg-9~0exp.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/experimental/arm64/khmer_3.0.0~a3+dfsg-9~0exp.diff.gz is missing [2024-09-28 13:34:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/experimental/armhf/khmer_3.0.0~a3+dfsg-9~0exp.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/experimental/armhf/khmer_3.0.0~a3+dfsg-9~0exp.diff.gz is missing [2024-09-28 13:34:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/experimental/i386/khmer_3.0.0~a3+dfsg-9~0exp.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/experimental/i386/khmer_3.0.0~a3+dfsg-9~0exp.diff.gz is missing [2024-09-28 13:34:52] INFO: Finished at 2024-09-28 13:34:52.009009, took: 0:00:00.723146 Sat Sep 28 13:34:52 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/khmer.html Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/khmer_3.0.0~a3+dfsg-8.rbuild.log: 91.3% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/khmer_3.0.0~a3+dfsg-8.rbuild.log.gz [2024-09-28 13:34:52] INFO: Starting at 2024-09-28 13:34:52.493244 [2024-09-28 13:34:52] INFO: Generating the pages of 1 package(s) [2024-09-28 13:34:52] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/khmer_3.0.0~a3+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/khmer_3.0.0~a3+dfsg-8.diff.gz is missing [2024-09-28 13:34:52] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/khmer_3.0.0~a3+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/khmer_3.0.0~a3+dfsg-8.diff.gz is missing [2024-09-28 13:34:52] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/khmer_3.0.0~a3+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/khmer_3.0.0~a3+dfsg-8.diff.gz is missing [2024-09-28 13:34:52] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/khmer_3.0.0~a3+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/khmer_3.0.0~a3+dfsg-8.diff.gz is missing [2024-09-28 13:34:52] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/khmer_3.0.0~a3+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/khmer_3.0.0~a3+dfsg-8.diff.gz is missing [2024-09-28 13:34:52] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/khmer_3.0.0~a3+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/khmer_3.0.0~a3+dfsg-8.diff.gz is missing [2024-09-28 13:34:52] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/armhf/khmer_3.0.0~a3+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/armhf/khmer_3.0.0~a3+dfsg-8.diff.gz is missing [2024-09-28 13:34:52] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/khmer_3.0.0~a3+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/khmer_3.0.0~a3+dfsg-8.diff.gz is missing [2024-09-28 13:34:53] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/arm64/khmer_3.0.0~a3+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/arm64/khmer_3.0.0~a3+dfsg-4.diff.gz is missing [2024-09-28 13:34:53] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/khmer_3.0.0~a3+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/khmer_3.0.0~a3+dfsg-4.diff.gz is missing [2024-09-28 13:34:53] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/i386/khmer_3.0.0~a3+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/i386/khmer_3.0.0~a3+dfsg-4.diff.gz is missing [2024-09-28 13:34:53] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/armhf/khmer_2.1.2+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/armhf/khmer_2.1.2+dfsg-8.diff.gz is missing [2024-09-28 13:34:53] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/i386/khmer_2.1.2+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/i386/khmer_2.1.2+dfsg-8.diff.gz is missing [2024-09-28 13:34:53] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/experimental/amd64/khmer_3.0.0~a3+dfsg-9~0exp.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/experimental/amd64/khmer_3.0.0~a3+dfsg-9~0exp.diff.gz is missing [2024-09-28 13:34:53] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/experimental/arm64/khmer_3.0.0~a3+dfsg-9~0exp.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/experimental/arm64/khmer_3.0.0~a3+dfsg-9~0exp.diff.gz is missing [2024-09-28 13:34:53] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/experimental/armhf/khmer_3.0.0~a3+dfsg-9~0exp.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/experimental/armhf/khmer_3.0.0~a3+dfsg-9~0exp.diff.gz is missing [2024-09-28 13:34:53] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/experimental/i386/khmer_3.0.0~a3+dfsg-9~0exp.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/experimental/i386/khmer_3.0.0~a3+dfsg-9~0exp.diff.gz is missing [2024-09-28 13:34:53] INFO: Finished at 2024-09-28 13:34:53.152287, took: 0:00:00.659049 All cleanup done. Sat Sep 28 13:34:53 UTC 2024 - total duration: 0h 16m 8s. Sat Sep 28 13:34:53 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-7zSkbnGH, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 16min 11.059s CPU time consumed: 6.523s