I: pbuilder: network access will be disabled during build I: Current time: Sun May 12 02:43:44 +14 2024 I: pbuilder-time-stamp: 1715431424 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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/816689/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 11 12:44 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/816689/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/816689/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=2bb7cf98b5c24567b7c2660473b0e135 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=816689 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.vI1rbC9W/pbuilderrc_305w --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.vI1rbC9W/b2 --logfile b2/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-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 11 11:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/816689/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 ... 19699 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} libbsd0{a} libbz2-dev{a} libdebhelper-perl{a} libedit2{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libicu72{a} libjs-bootstrap{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} libruby{a} libruby3.1t64{a} libsub-override-perl{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-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-dev{a} python3-distutils{a} python3-docutils{a} python3-guzzle-sphinx-theme{a} python3-idna{a} python3-imagesize{a} python3-iniconfig{a} python3-jinja2{a} python3-lib2to3{a} python3-markupsafe{a} python3-minimal{a} python3-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-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinxcontrib.autoprogram{a} python3-urllib3{a} python3.11{a} python3.11-dev{a} python3.11-minimal{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 libarchive-cpio-perl libgpm2 libjson-xs-perl libltdl-dev libmail-sendmail-perl libpaper-utils lynx python3-pil wget zip 0 packages upgraded, 125 newly installed, 0 to remove and 0 not upgraded. Need to get 73.1 MB of archives. After unpacking 311 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.3-1 [809 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.3-1 [2139 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 rubygems-integration all 1.18 [6704 B] Get: 30 http://deb.debian.org/debian trixie/main amd64 rake all 13.0.6-3 [83.9 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 ruby-sdbm amd64 1.0.0-5+b4 [15.4 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.4+20240414-1 [104 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libruby3.1t64 amd64 3.1.2-8.3 [5399 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 ruby3.1 amd64 3.1.2-8.3 [664 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libruby amd64 1:3.1+nmu1 [4664 B] Get: 42 http://deb.debian.org/debian trixie/main amd64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 ruby amd64 1:3.1+nmu1 [5584 B] Get: 44 http://deb.debian.org/debian trixie/main amd64 ruby-asciidoctor all 2.0.20-1 [212 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 asciidoctor all 2.0.20-1 [87.7 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 cython3 amd64 3.0.10+dfsg-5 [3571 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 59 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 dh-exec amd64 0.29 [25.4 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20240422 [107 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 docutils-common all 0.20.1+dfsg-3 [128 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 fonts-liberation all 1:2.1.5-3 [1475 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-5.1 [31.3 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.2-1 [155 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 7.2.6-6 [150 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libpython3.11t64 amd64 3.11.9-1 [1960 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libpython3.11-dev amd64 3.11.9-1 [4513 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.11.8-1 [9560 B] Get: 88 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.3-1 [1951 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libpython3.12t64 amd64 3.12.3-1 [2107 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libpython3.12-dev amd64 3.12.3-1 [5069 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libpython3-all-dev amd64 3.11.8-1 [1072 B] Get: 92 http://deb.debian.org/debian trixie/main amd64 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.3-1 [659 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.11.8-1 [1056 B] Get: 96 http://deb.debian.org/debian trixie/main amd64 python3.11-dev amd64 3.11.9-1 [501 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.11.8-1 [26.1 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 python3.12-dev amd64 3.12.3-1 [499 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 python3-all-dev amd64 3.11.8-1 [1072 B] Get: 100 http://deb.debian.org/debian trixie/main amd64 python3-babel all 2.14.0-1 [111 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2023.11.17-1 [155 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer all 3.3.2-1 [51.6 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 python3-roman all 3.3-3 [9880 B] Get: 105 http://deb.debian.org/debian trixie/main amd64 python3-docutils all 0.20.1+dfsg-3 [389 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 sphinx-common all 7.2.6-6 [702 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 108 http://deb.debian.org/debian trixie/main amd64 python3-markupsafe amd64 2.1.5-1 [14.5 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 python3-pygments all 2.17.2+dfsg-1 [818 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.6-2 [37.0 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 python3-six all 1.16.0-6 [16.3 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 1.26.18-2 [116 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.31.0+dfsg-1 [68.6 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 python3-sphinx all 7.2.6-6 [552 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 python3-guzzle-sphinx-theme all 0.7.11-6 [1346 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 120 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 7.4.4-3 [239 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 python3-pytest-runner all 2.11.1-4 [8432 B] Get: 123 http://deb.debian.org/debian trixie/main amd64 python3-screed all 1.1.3-1 [109 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 python3-sphinxcontrib.autoprogram all 0.1.8-2 [10.6 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 rdfind amd64 1.6.0-1+b1 [44.7 kB] Fetched 73.1 MB in 4s (18.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... 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 ... 20015 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_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 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... 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 ... 21007 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:amd64. 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Unpacking cython3 (3.0.10+dfsg-5) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../039-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../040-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../041-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../042-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../043-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../044-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../045-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../046-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../047-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../048-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../049-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../050-gettext_0.21-14+b1_amd64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../051-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../052-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../053-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package dh-exec. Preparing to unpack .../054-dh-exec_0.29_amd64.deb ... Unpacking dh-exec (0.29) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../055-python3-pkg-resources_68.1.2-2_all.deb ... Unpacking python3-pkg-resources (68.1.2-2) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../056-python3-lib2to3_3.12.3-1_all.deb ... Unpacking python3-lib2to3 (3.12.3-1) ... 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Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Selecting previously unselected package fonts-liberation. Preparing to unpack .../063-fonts-liberation_1%3a2.1.5-3_all.deb ... Unpacking fonts-liberation (1:2.1.5-3) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../064-libbz2-dev_1.0.8-5.1_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.8-5.1) ... Selecting previously unselected package libexpat1-dev:amd64. Preparing to unpack .../065-libexpat1-dev_2.6.2-1_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.6.2-1) ... Selecting previously unselected package libjs-bootstrap. Preparing to unpack .../066-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../067-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. 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Selecting previously unselected package libpython3-dev:amd64. Preparing to unpack .../074-libpython3-dev_3.11.8-1_amd64.deb ... Unpacking libpython3-dev:amd64 (3.11.8-1) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../075-libpython3.12-stdlib_3.12.3-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.3-1) ... Selecting previously unselected package libpython3.12t64:amd64. Preparing to unpack .../076-libpython3.12t64_3.12.3-1_amd64.deb ... Unpacking libpython3.12t64:amd64 (3.12.3-1) ... Selecting previously unselected package libpython3.12-dev:amd64. Preparing to unpack .../077-libpython3.12-dev_3.12.3-1_amd64.deb ... Unpacking libpython3.12-dev:amd64 (3.12.3-1) ... Selecting previously unselected package libpython3-all-dev:amd64. Preparing to unpack .../078-libpython3-all-dev_3.11.8-1_amd64.deb ... Unpacking libpython3-all-dev:amd64 (3.11.8-1) ... Selecting previously unselected package python-babel-localedata. 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Preparing to unpack .../085-python3.12-dev_3.12.3-1_amd64.deb ... Unpacking python3.12-dev (3.12.3-1) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../086-python3-all-dev_3.11.8-1_amd64.deb ... Unpacking python3-all-dev (3.11.8-1) ... Selecting previously unselected package python3-babel. Preparing to unpack .../087-python3-babel_2.14.0-1_all.deb ... Unpacking python3-babel (2.14.0-1) ... Selecting previously unselected package python3-certifi. Preparing to unpack .../088-python3-certifi_2023.11.17-1_all.deb ... Unpacking python3-certifi (2023.11.17-1) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../089-python3-chardet_5.2.0+dfsg-1_all.deb ... Unpacking python3-chardet (5.2.0+dfsg-1) ... Selecting previously unselected package python3-charset-normalizer. Preparing to unpack .../090-python3-charset-normalizer_3.3.2-1_all.deb ... Unpacking python3-charset-normalizer (3.3.2-1) ... 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Unpacking python3-pytest (7.4.4-3) ... Selecting previously unselected package python3-pytest-runner. Preparing to unpack .../109-python3-pytest-runner_2.11.1-4_all.deb ... Unpacking python3-pytest-runner (2.11.1-4) ... Selecting previously unselected package python3-screed. Preparing to unpack .../110-python3-screed_1.1.3-1_all.deb ... Unpacking python3-screed (1.1.3-1) ... Selecting previously unselected package python3-sphinxcontrib.autoprogram. Preparing to unpack .../111-python3-sphinxcontrib.autoprogram_0.1.8-2_all.deb ... Unpacking python3-sphinxcontrib.autoprogram (0.1.8-2) ... Selecting previously unselected package rdfind. Preparing to unpack .../112-rdfind_1.6.0-1+b1_amd64.deb ... Unpacking rdfind (1.6.0-1+b1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1+b1) ... Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Setting up libdebhelper-perl (13.15.3) ... Setting up rdfind (1.6.0-1+b1) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpython3.12-minimal:amd64 (3.12.3-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up python-babel-localedata (2.14.0-1) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sat May 11 12:46:27 UTC 2024. Universal Time is now: Sat May 11 12:46:27 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libexpat1-dev:amd64 (2.6.2-1) ... Setting up libncurses6:amd64 (6.4+20240414-1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up ruby-webrick (1.8.1-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... 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 libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libbz2-dev:amd64 (1.0.8-5.1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.12-minimal (3.12.3-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libedit2:amd64 (3.1-20230828-1+b1) ... 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 libjs-sphinxdoc (7.2.6-6) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up xml-core (0.19) ... Setting up libpython3.12-stdlib:amd64 (3.12.3-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libpython3.11t64:amd64 (3.11.9-1) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3.12t64:amd64 (3.12.3-1) ... Setting up libpython3.11-dev:amd64 (3.11.9-1) ... Setting up sphinx-common (7.2.6-6) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libpython3-dev:amd64 (3.11.8-1) ... Setting up python3.11-dev (3.11.9-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up dh-exec (0.29) ... Setting up libpython3.12-dev:amd64 (3.12.3-1) ... Setting up python3-markupsafe (2.1.5-1) ... Setting up python3-six (1.16.0-6) ... Setting up python3-roman (3.3-3) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.0-1) ... Setting up python3-certifi (2023.11.17-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up libpython3-all-dev:amd64 (3.11.8-1) ... Setting up python3-idna (3.6-2) ... Setting up python3.12-dev (3.12.3-1) ... Setting up cython3 (3.0.10+dfsg-5) ... Setting up python3-urllib3 (1.26.18-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-screed (1.1.3-1) ... 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-charset-normalizer (3.3.2-1) ... Setting up python3-pytest (7.4.4-3) ... Setting up python3-alabaster (0.7.12-1) ... Setting up python3-all (3.11.8-1) ... Setting up python3-pygments (2.17.2+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-dev (3.11.8-1) ... Setting up python3-requests (2.31.0+dfsg-1) ... Setting up python3-pytest-runner (2.11.1-4) ... Setting up dh-python (6.20240422) ... Setting up python3-all-dev (3.11.8-1) ... Setting up rake (13.0.6-3) ... Setting up ruby3.1 (3.1.2-8.3) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b4) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up libruby3.1t64:amd64 (3.1.2-8.3) ... Setting up libruby:amd64 (1:3.1+nmu1) ... Setting up ruby (1:3.1+nmu1) ... Setting up ruby-asciidoctor (2.0.20-1) ... Setting up asciidoctor (2.0.20-1) ... Processing triggers for libc-bin (2.38-7) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.20.1+dfsg-3) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.20.1+dfsg-3) ... Setting up python3-sphinx (7.2.6-6) ... Setting up python3-guzzle-sphinx-theme (0.7.11-6) ... Setting up python3-sphinxcontrib.autoprogram (0.1.8-2) ... 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: user script /srv/workspace/pbuilder/816689/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/816689/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/khmer-3.0.0~a3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../khmer_3.0.0~a3+dfsg-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 3.11" 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:744: 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:84: _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) WARNING: The wheel package is not available. /usr/lib/python3/dist-packages/setuptools/dist.py:744: 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 I: pybuild base:311: python3.11 setup.py clean *** NOTE: Found Cython, extension files will be transpiled if this is an install invocation. /usr/lib/python3/dist-packages/setuptools/dist.py:744: 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:84: _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) WARNING: The wheel package is not available. /usr/lib/python3/dist-packages/setuptools/dist.py:744: 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_3.11_khmer/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; cd src/oxli && /usr/bin/make clean make[2]: Entering directory '/build/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 3.11" 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:744: 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:84: _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) WARNING: The wheel package is not available. /usr/lib/python3/dist-packages/setuptools/dist.py:744: 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 I: pybuild base:311: python3.11 setup.py config *** NOTE: Found Cython, extension files will be transpiled if this is an install invocation. /usr/lib/python3/dist-packages/setuptools/dist.py:744: 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:84: _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) WARNING: The wheel package is not available. /usr/lib/python3/dist-packages/setuptools/dist.py:744: 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 3.11" I: pybuild base:311: /usr/bin/python3.12 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:744: 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:84: _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) WARNING: The wheel package is not available. /usr/lib/python3/dist-packages/setuptools/dist.py:744: 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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor 'oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)': include/oxli/assembler.hh:80:23: warning: 'oxli::LinearAssembler::graph' will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ include/oxli/assembler.hh:79:16: warning: 'oxli::WordLength oxli::LinearAssembler::_ksize' [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor 'oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()': src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type 'oxli::LinearAssembler' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh: In constructor 'oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)': include/oxli/assembler.hh:158:16: warning: 'oxli::JunctionCountAssembler::_ksize' will be initialized after [-Wreorder] 158 | WordLength _ksize; | ^~~~~~ include/oxli/assembler.hh:153:15: warning: 'oxli::Traverser oxli::JunctionCountAssembler::traverser' [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh:153:15: warning: 'oxli::JunctionCountAssembler::traverser' will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ include/oxli/assembler.hh:151:21: warning: 'oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm' [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:626:1: required from here src/oxli/hashtable.cc:138:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 138 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:643:1: required from here src/oxli/hashtable.cc:208:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 208 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_with_mask(oxli::read_parsers::ReadParserPtr&, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:662:1: required from here src/oxli/hashtable.cc:168:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 168 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding_with_mask(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:685:1: required from here src/oxli/hashtable.cc:250:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 250 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/hllcounter.cc: In instantiation of 'void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hllcounter.cc:435:1: required from here src/oxli/hllcounter.cc:366:40: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 366 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/read_aligner.cc:48: include/oxli/read_aligner.hh:114:15: warning: 'oxli::freq_default' defined but not used [-Wunused-variable] 114 | static double freq_default[] = { log2(0.955), | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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++/13/memory:78, from third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from src/oxli/read_parsers.cc:38: /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/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++/13/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++/13/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++/13/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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61: third-party/seqan/core/include/seqan/store/store_all.h: In function 'void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)': third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 1733 | if (alignQualityStoreLengthPre == 0u) | ^~ third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/subset.cc: In member function 'size_t oxli::SubsetPartition::output_partitioned_file(const std::string&, const std::string&, bool, oxli::CallbackFn, void*)': src/oxli/subset.cc:136:24: warning: unused variable 'ksize' [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:202:5: required from here include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ src/oxli/traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:203:5: required from here include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -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 -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -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 -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:1334: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/assembly.cpp:1206: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/assembly.cpp:1215: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/assembly.cpp:1212: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -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 -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/legacy_partitioning.cpp:1333: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/legacy_partitioning.cpp:1205: note: this is the location of the previous definition 1205 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/legacy_partitioning.cpp:1214: note: this is the location of the previous definition 1214 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/legacy_partitioning.cpp:1211: note: this is the location of the previous definition 1211 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -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 -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/include/c++/13/set:62, from khmer/_oxli/hashset.cpp:1310: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_lower_bound(_Link_type, _Base_ptr, const _Key&) [with _Key = long long unsigned int; _Val = long long unsigned int; _KeyOfValue = std::_Identity; _Compare = std::less; _Alloc = std::allocator]', inlined from 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::find(const _Key&) [with _Key = long long unsigned int; _Val = long long unsigned int; _KeyOfValue = std::_Identity; _Compare = std::less; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_tree.h:2532:36, inlined from 'std::set<_Key, _Compare, _Alloc>::iterator std::set<_Key, _Compare, _Alloc>::find(const key_type&) [with _Key = long long unsigned int; _Compare = std::less; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_set.h:797:25, inlined from 'int __pyx_pf_5khmer_5_oxli_7hashset_7HashSet_10__contains__(__pyx_obj_5khmer_5_oxli_7hashset_HashSet*, PyObject*)' at khmer/_oxli/hashset.cpp:4140:35, inlined from 'int __pyx_pw_5khmer_5_oxli_7hashset_7HashSet_11__contains__(PyObject*, PyObject*)' at khmer/_oxli/hashset.cpp:4010:68: /usr/include/c++/13/bits/stl_tree.h:1952:9: warning: '__pyx_v_h' may be used uninitialized [-Wmaybe-uninitialized] 1952 | if (!_M_impl._M_key_compare(_S_key(__x), __k)) | ^~ khmer/_oxli/hashset.cpp: In function 'int __pyx_pw_5khmer_5_oxli_7hashset_7HashSet_11__contains__(PyObject*, PyObject*)': khmer/_oxli/hashset.cpp:4018:22: note: '__pyx_v_h' was declared here 4018 | oxli::HashIntoType __pyx_v_h; | ^~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -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 -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/parsing.cpp:1321: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/parsing.cpp:1199: note: this is the location of the previous definition 1199 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/parsing.cpp:1208: note: this is the location of the previous definition 1208 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/parsing.cpp:1205: note: this is the location of the previous definition 1205 | #define PyInt_FromLong PyLong_FromLong | khmer/_oxli/parsing.cpp: In function 'bool __pyx_f_5khmer_5_oxli_7parsing_sanitize_sequence(std::string&, std::string&, bool)': khmer/_oxli/parsing.cpp:8651:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 8651 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { | ~~~~~~~~~~^~~~~~~~~~~ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -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 -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -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 -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/labeling.cpp:1333: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/labeling.cpp:1205: note: this is the location of the previous definition 1205 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/labeling.cpp:1214: note: this is the location of the previous definition 1214 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/labeling.cpp:1211: note: this is the location of the previous definition 1211 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -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 -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/readaligner.cpp:1334: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/readaligner.cpp:1206: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/readaligner.cpp:1215: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/readaligner.cpp:1212: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -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 -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:1334: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/graphs.cpp:1206: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/graphs.cpp:1215: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/graphs.cpp:1212: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -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 -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/traversal.cpp:1334: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/traversal.cpp:1206: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/traversal.cpp:1215: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/traversal.cpp:1212: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -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 -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/hllcounter.cpp:1327: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/hllcounter.cpp:1201: note: this is the location of the previous definition 1201 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/hllcounter.cpp:1210: note: this is the location of the previous definition 1210 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/hllcounter.cpp:1207: note: this is the location of the previous definition 1207 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -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 -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 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:744: 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:84: _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) WARNING: The wheel package is not available. /usr/lib/python3/dist-packages/setuptools/dist.py:744: 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_3.11_khmer/build/khmer copying khmer/kfile.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer copying khmer/khmer_logger.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer copying khmer/khmer_args.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer copying khmer/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer copying khmer/trimming.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer copying khmer/utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer copying khmer/_version.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer copying khmer/thread_utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_lump.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_memory.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_oxli_functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_qfstorage.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_nibblestorage.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_subset_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_version.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_read_handling.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_sequence_validation.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_script_output.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_read_parsers.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_sandbox_scripts.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_normalize_by_median.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_scripts.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_hashset.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_banding.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_counttable.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_script_arguments.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/graph_features.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_cython_parsing.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_threaded_sequence_processor.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_hll.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_counting_single.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_countgraph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_tabletype.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_labelhash.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_cpython_hierarchy.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_read_aligner.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_filter_abund.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/khmer_tst_utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_assembly.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_nodegraph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/table_fixtures.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests copying tests/test_streaming_io.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli copying oxli/build_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli copying oxli/partition.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli copying oxli/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli copying oxli/functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli 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 tests/.gitignore -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.truncated.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.truncated.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/README.rst -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/all-A.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k12.ct -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k12.ht -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k32.stoptags -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k32.tagset -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/banding-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/bogus.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/branched-genome.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/fakelump.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/fakelump.fa.stoptags.txt -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/filter-test-A.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/filter-test-B.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k12.ht -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k32.stoptags -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k32.tagset -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/multi-output.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/normC20k20.ct -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/old-style-format-w-comments.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.badleft -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.badright -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.paired_bad -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken2.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken2.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken3.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken3.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken4.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken4.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-2.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-broken.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-witherror.fa.pe -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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_3.11_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_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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_3.11_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_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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_3.11_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_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/paired.malformat.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/readaligner-default.json -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/readaligner-k12.json -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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_3.11_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_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/seq-a.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/seq-b.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/simple-genome.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/single-read.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/single-read.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-empty.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph5.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-labels.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-large.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-multi.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-overlap1.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-overlap2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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_3.11_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_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-short.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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_3.11_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_3.11_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_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/test-transcript.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/truncated.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data copying tests/test-data/unclean-reads.fastq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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_3.11_khmer/build/khmer/tests/test-data copying khmer/_oxli/assembly.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/assembly.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/assembly.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/hashset.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/hashset.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/hashset.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/hllcounter.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/hllcounter.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/hllcounter.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/labeling.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/labeling.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/labeling.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/legacy_partitioning.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/legacy_partitioning.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/legacy_partitioning.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/oxli_exception_convert.cc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/oxli_exception_convert.hh -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/oxli_types.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/readaligner.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/readaligner.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/readaligner.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/traversal.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/traversal.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/traversal.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/utils.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/utils.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli copying khmer/_oxli/utils.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli UPDATING /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_version.py set /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_version.py to '3.0.0a3' running build_ext bash -c "cd third-party/cqf && make" make[2]: Entering directory '/build/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 creating build/temp.linux-x86_64-cpython-311 creating build/temp.linux-x86_64-cpython-311/src creating build/temp.linux-x86_64-cpython-311/src/khmer creating build/temp.linux-x86_64-cpython-311/src/oxli creating build/temp.linux-x86_64-cpython-311/third-party creating build/temp.linux-x86_64-cpython-311/third-party/smhasher x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor 'oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)': include/oxli/assembler.hh:80:23: warning: 'oxli::LinearAssembler::graph' will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ include/oxli/assembler.hh:79:16: warning: 'oxli::WordLength oxli::LinearAssembler::_ksize' [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor 'oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()': src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type 'oxli::LinearAssembler' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh: In constructor 'oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)': include/oxli/assembler.hh:158:16: warning: 'oxli::JunctionCountAssembler::_ksize' will be initialized after [-Wreorder] 158 | WordLength _ksize; | ^~~~~~ include/oxli/assembler.hh:153:15: warning: 'oxli::Traverser oxli::JunctionCountAssembler::traverser' [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh:153:15: warning: 'oxli::JunctionCountAssembler::traverser' will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ include/oxli/assembler.hh:151:21: warning: 'oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm' [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:626:1: required from here src/oxli/hashtable.cc:138:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 138 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:643:1: required from here src/oxli/hashtable.cc:208:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 208 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_with_mask(oxli::read_parsers::ReadParserPtr&, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:662:1: required from here src/oxli/hashtable.cc:168:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 168 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding_with_mask(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:685:1: required from here src/oxli/hashtable.cc:250:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 250 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/hllcounter.cc: In instantiation of 'void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hllcounter.cc:435:1: required from here src/oxli/hllcounter.cc:366:40: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 366 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/read_aligner.cc:48: include/oxli/read_aligner.hh:114:15: warning: 'oxli::freq_default' defined but not used [-Wunused-variable] 114 | static double freq_default[] = { log2(0.955), | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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++/13/memory:78, from third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from src/oxli/read_parsers.cc:38: /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/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++/13/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++/13/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++/13/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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61: third-party/seqan/core/include/seqan/store/store_all.h: In function 'void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)': third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 1733 | if (alignQualityStoreLengthPre == 0u) | ^~ third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/storage.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/subset.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/subset.cc: In member function 'size_t oxli::SubsetPartition::output_partitioned_file(const std::string&, const std::string&, bool, oxli::CallbackFn, void*)': src/oxli/subset.cc:136:24: warning: unused variable 'ksize' [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:202:5: required from here include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ src/oxli/traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:203:5: required from here include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_khmer.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hashing' extension creating build/temp.linux-x86_64-cpython-311/khmer creating build/temp.linux-x86_64-cpython-311/khmer/_oxli x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/hashing.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/hashing.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/hashing.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashing.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.assembly' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/assembly.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/assembly.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:1334: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/assembly.cpp:1206: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/assembly.cpp:1215: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/assembly.cpp:1212: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/assembly.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.legacy_partitioning' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/legacy_partitioning.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/legacy_partitioning.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/legacy_partitioning.cpp:1333: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/legacy_partitioning.cpp:1205: note: this is the location of the previous definition 1205 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/legacy_partitioning.cpp:1214: note: this is the location of the previous definition 1214 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/legacy_partitioning.cpp:1211: note: this is the location of the previous definition 1211 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/legacy_partitioning.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hashset' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/hashset.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/hashset.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/include/c++/13/set:62, from khmer/_oxli/hashset.cpp:1310: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_lower_bound(_Link_type, _Base_ptr, const _Key&) [with _Key = long long unsigned int; _Val = long long unsigned int; _KeyOfValue = std::_Identity; _Compare = std::less; _Alloc = std::allocator]', inlined from 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::find(const _Key&) [with _Key = long long unsigned int; _Val = long long unsigned int; _KeyOfValue = std::_Identity; _Compare = std::less; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_tree.h:2532:36, inlined from 'std::set<_Key, _Compare, _Alloc>::iterator std::set<_Key, _Compare, _Alloc>::find(const key_type&) [with _Key = long long unsigned int; _Compare = std::less; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_set.h:797:25, inlined from 'int __pyx_pf_5khmer_5_oxli_7hashset_7HashSet_10__contains__(__pyx_obj_5khmer_5_oxli_7hashset_HashSet*, PyObject*)' at khmer/_oxli/hashset.cpp:4140:35, inlined from 'int __pyx_pw_5khmer_5_oxli_7hashset_7HashSet_11__contains__(PyObject*, PyObject*)' at khmer/_oxli/hashset.cpp:4010:68: /usr/include/c++/13/bits/stl_tree.h:1952:9: warning: '__pyx_v_h' may be used uninitialized [-Wmaybe-uninitialized] 1952 | if (!_M_impl._M_key_compare(_S_key(__x), __k)) | ^~ khmer/_oxli/hashset.cpp: In function 'int __pyx_pw_5khmer_5_oxli_7hashset_7HashSet_11__contains__(PyObject*, PyObject*)': khmer/_oxli/hashset.cpp:4018:22: note: '__pyx_v_h' was declared here 4018 | oxli::HashIntoType __pyx_v_h; | ^~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/hashset.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashset.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.parsing' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/parsing.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/parsing.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/parsing.cpp:1321: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/parsing.cpp:1199: note: this is the location of the previous definition 1199 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/parsing.cpp:1208: note: this is the location of the previous definition 1208 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/parsing.cpp:1205: note: this is the location of the previous definition 1205 | #define PyInt_FromLong PyLong_FromLong | khmer/_oxli/parsing.cpp: In function 'bool __pyx_f_5khmer_5_oxli_7parsing_sanitize_sequence(std::string&, std::string&, bool)': khmer/_oxli/parsing.cpp:8651:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 8651 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { | ~~~~~~~~~~^~~~~~~~~~~ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/parsing.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/parsing.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.utils' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/utils.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/utils.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.labeling' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/labeling.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/labeling.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/labeling.cpp:1333: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/labeling.cpp:1205: note: this is the location of the previous definition 1205 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/labeling.cpp:1214: note: this is the location of the previous definition 1214 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/labeling.cpp:1211: note: this is the location of the previous definition 1211 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/labeling.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.readaligner' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/readaligner.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/readaligner.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/readaligner.cpp:1334: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/readaligner.cpp:1206: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/readaligner.cpp:1215: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/readaligner.cpp:1212: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/readaligner.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.graphs' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/graphs.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/graphs.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:1334: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/graphs.cpp:1206: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/graphs.cpp:1215: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/graphs.cpp:1212: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/graphs.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.traversal' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/traversal.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/traversal.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/traversal.cpp:1334: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/traversal.cpp:1206: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/traversal.cpp:1215: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/traversal.cpp:1212: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hllcounter' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/hllcounter.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/hllcounter.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/hllcounter.cpp:1327: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/hllcounter.cpp:1201: note: this is the location of the previous definition 1201 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/hllcounter.cpp:1210: note: this is the location of the previous definition 1210 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/hllcounter.cpp:1207: note: this is the location of the previous definition 1207 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hllcounter.cpython-311-x86_64-linux-gnu.so -fopenmp running build_scripts creating build/scripts-3.11 copying and adjusting scripts/unique-kmers.py -> build/scripts-3.11 copying and adjusting scripts/count-median.py -> build/scripts-3.11 copying and adjusting scripts/load-into-counting.py -> build/scripts-3.11 copying and adjusting scripts/normalize-by-median.py -> build/scripts-3.11 copying and adjusting scripts/make-initial-stoptags.py -> build/scripts-3.11 copying and adjusting scripts/extract-paired-reads.py -> build/scripts-3.11 copying and adjusting scripts/sample-reads-randomly.py -> build/scripts-3.11 copying and adjusting scripts/abundance-dist.py -> build/scripts-3.11 copying and adjusting scripts/partition-graph.py -> build/scripts-3.11 copying and adjusting scripts/extract-partitions.py -> build/scripts-3.11 copying and adjusting scripts/filter-abund.py -> build/scripts-3.11 copying and adjusting scripts/readstats.py -> build/scripts-3.11 copying and adjusting scripts/trim-low-abund.py -> build/scripts-3.11 copying and adjusting scripts/merge-partitions.py -> build/scripts-3.11 copying and adjusting scripts/abundance-dist-single.py -> build/scripts-3.11 copying and adjusting scripts/interleave-reads.py -> build/scripts-3.11 copying and adjusting scripts/find-knots.py -> build/scripts-3.11 copying and adjusting scripts/fastq-to-fasta.py -> build/scripts-3.11 copying and adjusting scripts/load-graph.py -> build/scripts-3.11 copying and adjusting scripts/extract-long-sequences.py -> build/scripts-3.11 copying and adjusting scripts/split-paired-reads.py -> build/scripts-3.11 copying and adjusting scripts/do-partition.py -> build/scripts-3.11 copying and adjusting scripts/annotate-partitions.py -> build/scripts-3.11 copying and adjusting scripts/filter-stoptags.py -> build/scripts-3.11 copying and adjusting scripts/filter-abund-single.py -> build/scripts-3.11 changing mode of build/scripts-3.11/unique-kmers.py from 644 to 755 changing mode of build/scripts-3.11/count-median.py from 644 to 755 changing mode of build/scripts-3.11/load-into-counting.py from 644 to 755 changing mode of build/scripts-3.11/normalize-by-median.py from 644 to 755 changing mode of build/scripts-3.11/make-initial-stoptags.py from 644 to 755 changing mode of build/scripts-3.11/extract-paired-reads.py from 644 to 755 changing mode of build/scripts-3.11/sample-reads-randomly.py from 644 to 755 changing mode of build/scripts-3.11/abundance-dist.py from 644 to 755 changing mode of build/scripts-3.11/partition-graph.py from 644 to 755 changing mode of build/scripts-3.11/extract-partitions.py from 644 to 755 changing mode of build/scripts-3.11/filter-abund.py from 644 to 755 changing mode of build/scripts-3.11/readstats.py from 644 to 755 changing mode of build/scripts-3.11/trim-low-abund.py from 644 to 755 changing mode of build/scripts-3.11/merge-partitions.py from 644 to 755 changing mode of build/scripts-3.11/abundance-dist-single.py from 644 to 755 changing mode of build/scripts-3.11/interleave-reads.py from 644 to 755 changing mode of build/scripts-3.11/find-knots.py from 644 to 755 changing mode of build/scripts-3.11/fastq-to-fasta.py from 644 to 755 changing mode of build/scripts-3.11/load-graph.py from 644 to 755 changing mode of build/scripts-3.11/extract-long-sequences.py from 644 to 755 changing mode of build/scripts-3.11/split-paired-reads.py from 644 to 755 changing mode of build/scripts-3.11/do-partition.py from 644 to 755 changing mode of build/scripts-3.11/annotate-partitions.py from 644 to 755 changing mode of build/scripts-3.11/filter-stoptags.py from 644 to 755 changing mode of build/scripts-3.11/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:744: 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:84: _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) WARNING: The wheel package is not available. /usr/lib/python3/dist-packages/setuptools/dist.py:744: 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:40: 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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor 'oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)': include/oxli/assembler.hh:80:23: warning: 'oxli::LinearAssembler::graph' will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ include/oxli/assembler.hh:79:16: warning: 'oxli::WordLength oxli::LinearAssembler::_ksize' [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor 'oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()': src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type 'oxli::LinearAssembler' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh: In constructor 'oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)': include/oxli/assembler.hh:158:16: warning: 'oxli::JunctionCountAssembler::_ksize' will be initialized after [-Wreorder] 158 | WordLength _ksize; | ^~~~~~ include/oxli/assembler.hh:153:15: warning: 'oxli::Traverser oxli::JunctionCountAssembler::traverser' [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh:153:15: warning: 'oxli::JunctionCountAssembler::traverser' will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ include/oxli/assembler.hh:151:21: warning: 'oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm' [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:626:1: required from here src/oxli/hashtable.cc:138:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 138 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:643:1: required from here src/oxli/hashtable.cc:208:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 208 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_with_mask(oxli::read_parsers::ReadParserPtr&, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:662:1: required from here src/oxli/hashtable.cc:168:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 168 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding_with_mask(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:685:1: required from here src/oxli/hashtable.cc:250:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 250 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/hllcounter.cc: In instantiation of 'void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hllcounter.cc:435:1: required from here src/oxli/hllcounter.cc:366:40: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 366 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/read_aligner.cc:48: include/oxli/read_aligner.hh:114:15: warning: 'oxli::freq_default' defined but not used [-Wunused-variable] 114 | static double freq_default[] = { log2(0.955), | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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++/13/memory:78, from third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from src/oxli/read_parsers.cc:38: /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/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++/13/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++/13/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++/13/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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61: third-party/seqan/core/include/seqan/store/store_all.h: In function 'void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)': third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 1733 | if (alignQualityStoreLengthPre == 0u) | ^~ third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/storage.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/subset.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/subset.cc: In member function 'size_t oxli::SubsetPartition::output_partitioned_file(const std::string&, const std::string&, bool, oxli::CallbackFn, void*)': src/oxli/subset.cc:136:24: warning: unused variable 'ksize' [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:202:5: required from here include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ src/oxli/traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:203:5: required from here include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ creating build/lib.linux-x86_64-cpython-311 creating build/lib.linux-x86_64-cpython-311/khmer x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_khmer.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hashing' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/hashing.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/hashing.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ creating build/lib.linux-x86_64-cpython-311/khmer/_oxli x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/hashing.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/hashing.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.assembly' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/assembly.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/assembly.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:1334: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/assembly.cpp:1206: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/assembly.cpp:1215: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/assembly.cpp:1212: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/assembly.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.legacy_partitioning' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/legacy_partitioning.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/legacy_partitioning.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/legacy_partitioning.cpp:1333: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/legacy_partitioning.cpp:1205: note: this is the location of the previous definition 1205 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/legacy_partitioning.cpp:1214: note: this is the location of the previous definition 1214 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/legacy_partitioning.cpp:1211: note: this is the location of the previous definition 1211 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/legacy_partitioning.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hashset' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/hashset.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/hashset.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/include/c++/13/set:62, from khmer/_oxli/hashset.cpp:1310: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_lower_bound(_Link_type, _Base_ptr, const _Key&) [with _Key = long long unsigned int; _Val = long long unsigned int; _KeyOfValue = std::_Identity; _Compare = std::less; _Alloc = std::allocator]', inlined from 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::find(const _Key&) [with _Key = long long unsigned int; _Val = long long unsigned int; _KeyOfValue = std::_Identity; _Compare = std::less; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_tree.h:2532:36, inlined from 'std::set<_Key, _Compare, _Alloc>::iterator std::set<_Key, _Compare, _Alloc>::find(const key_type&) [with _Key = long long unsigned int; _Compare = std::less; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_set.h:797:25, inlined from 'int __pyx_pf_5khmer_5_oxli_7hashset_7HashSet_10__contains__(__pyx_obj_5khmer_5_oxli_7hashset_HashSet*, PyObject*)' at khmer/_oxli/hashset.cpp:4140:35, inlined from 'int __pyx_pw_5khmer_5_oxli_7hashset_7HashSet_11__contains__(PyObject*, PyObject*)' at khmer/_oxli/hashset.cpp:4010:68: /usr/include/c++/13/bits/stl_tree.h:1952:9: warning: '__pyx_v_h' may be used uninitialized [-Wmaybe-uninitialized] 1952 | if (!_M_impl._M_key_compare(_S_key(__x), __k)) | ^~ khmer/_oxli/hashset.cpp: In function 'int __pyx_pw_5khmer_5_oxli_7hashset_7HashSet_11__contains__(PyObject*, PyObject*)': khmer/_oxli/hashset.cpp:4018:22: note: '__pyx_v_h' was declared here 4018 | oxli::HashIntoType __pyx_v_h; | ^~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/hashset.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/hashset.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.parsing' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/parsing.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/parsing.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/parsing.cpp:1321: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/parsing.cpp:1199: note: this is the location of the previous definition 1199 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/parsing.cpp:1208: note: this is the location of the previous definition 1208 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/parsing.cpp:1205: note: this is the location of the previous definition 1205 | #define PyInt_FromLong PyLong_FromLong | khmer/_oxli/parsing.cpp: In function 'bool __pyx_f_5khmer_5_oxli_7parsing_sanitize_sequence(std::string&, std::string&, bool)': khmer/_oxli/parsing.cpp:8651:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 8651 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { | ~~~~~~~~~~^~~~~~~~~~~ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/parsing.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/parsing.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.utils' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/utils.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/utils.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.labeling' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/labeling.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/labeling.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/labeling.cpp:1333: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/labeling.cpp:1205: note: this is the location of the previous definition 1205 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/labeling.cpp:1214: note: this is the location of the previous definition 1214 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/labeling.cpp:1211: note: this is the location of the previous definition 1211 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/labeling.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.readaligner' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/readaligner.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/readaligner.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/readaligner.cpp:1334: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/readaligner.cpp:1206: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/readaligner.cpp:1215: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/readaligner.cpp:1212: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/readaligner.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.graphs' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/graphs.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/graphs.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:1334: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/graphs.cpp:1206: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/graphs.cpp:1215: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/graphs.cpp:1212: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/graphs.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.traversal' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/traversal.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/traversal.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/traversal.cpp:1334: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/traversal.cpp:1206: note: this is the location of the previous definition 1206 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/traversal.cpp:1215: note: this is the location of the previous definition 1215 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/traversal.cpp:1212: note: this is the location of the previous definition 1212 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hllcounter' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/hllcounter.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/hllcounter.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/hllcounter.cpp:1327: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/hllcounter.cpp:1201: note: this is the location of the previous definition 1201 | #define PyInt_Check(op) PyLong_Check(op) | include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/hllcounter.cpp:1210: note: this is the location of the previous definition 1210 | #define PyInt_AsLong PyLong_AsLong | include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/hllcounter.cpp:1207: note: this is the location of the previous definition 1207 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c khmer/_oxli/oxli_exception_convert.cc -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/khmer/_oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o build/lib.linux-x86_64-cpython-311/khmer/_oxli/hllcounter.cpython-311-x86_64-linux-gnu.so -fopenmp copying build/lib.linux-x86_64-cpython-311/khmer/_khmer.cpython-311-x86_64-linux-gnu.so -> khmer copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/hashing.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/hashset.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/parsing.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-cpython-311/khmer/_oxli/hllcounter.cpython-311-x86_64-linux-gnu.so -> khmer/_oxli Creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/fakehome/.local/lib/python3.11/site-packages/khmer.egg-link (link to .) Adding khmer 3.0.0a3 to easy-install.pth file Installing 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 v7.2.6 making output directory... done 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 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... [ 50%] user/partitioning-workflow.png copying images... [100%] user/artifact-removal.png dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 10 warnings. The HTML pages are in build/sphinx/html. asciidoctor --backend manpage -a reproducible debian/khmer.1.adoc /usr/bin/make -C src/oxli clean make[2]: Entering directory '/build/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 hashtable.cc:138:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 138 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': hashtable.cc:643:1: required from here hashtable.cc:208:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 208 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_with_mask(oxli::read_parsers::ReadParserPtr&, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': hashtable.cc:662:1: required from here hashtable.cc:168:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 168 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding_with_mask(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': hashtable.cc:685:1: required from here hashtable.cc:250:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 250 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from hashtable.cc:49: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/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++/13/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from ../../include/oxli/hashgraph.hh:52, from hashgraph.cc:47: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/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 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++/13/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from hllcounter.cc:48: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/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++/13/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from kmer_hash.cc:49: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/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++/13/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from ../../include/oxli/hashgraph.hh:52, from labelhash.cc:44: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/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 ../../include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ ../../include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]': traversal.cc:203:5: required from here ../../include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ ../../include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from traversal.cc:38: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/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++/13/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from read_aligner.cc:46: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from read_aligner.cc:48: ../../include/oxli/read_aligner.hh:114:15: warning: 'oxli::freq_default' defined but not used [-Wunused-variable] 114 | static double freq_default[] = { log2(0.955), | ^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/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++/13/memory:78, from ../../third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from read_parsers.cc:38: /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/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++/13/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++/13/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++/13/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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from ../../include/oxli/hashgraph.hh:52, from subset.cc:47: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/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++/13/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from kmer_filters.cc:40: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/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++/13/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/assembler.hh:43: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/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++/13/cassert:44, from ../../third-party/rollinghash/characterhash.h:4, from ../../third-party/rollinghash/cyclichash.h:4, from ../../include/oxli/kmer_hash.hh:47, from ../../include/oxli/hashtable.hh:56, from storage.cc:44: ../../third-party/rollinghash/characterhash.h: In instantiation of 'hashvaluetype maskfnc(int) [with hashvaluetype = long unsigned int]': ../../third-party/rollinghash/cyclichash.h:30:38: required from 'CyclicHash::CyclicHash(int) [with hashvaluetype = long unsigned int; chartype = unsigned char]' ../../include/oxli/kmer_hash.hh:434:30: required from here ../../third-party/rollinghash/characterhash.h:14:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 14 | assert(bits <= sizeof(hashvaluetype) * 8); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/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 3.11" --dest-dir /build/reproducible-path/khmer-3.0.0\~a3\+dfsg/debian/tmp I: pybuild base:311: /usr/bin/python3.12 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:744: 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:84: _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) WARNING: The wheel package is not available. /usr/lib/python3/dist-packages/setuptools/dist.py:744: 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' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'khmer.build.khmer._oxli' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'khmer.build.khmer._oxli' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'khmer.build.khmer._oxli' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'khmer.build.khmer._oxli' to be distributed and are already explicitly excluding 'khmer.build.khmer._oxli' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/build creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/build/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/build/khmer/_oxli copying khmer/build/khmer/_oxli/oxli_exception_convert.hh -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/build/khmer/_oxli 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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor 'oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)': include/oxli/assembler.hh:80:23: warning: 'oxli::LinearAssembler::graph' will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ include/oxli/assembler.hh:79:16: warning: 'oxli::WordLength oxli::LinearAssembler::_ksize' [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor 'oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()': src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type 'oxli::LinearAssembler' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh: In constructor 'oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)': include/oxli/assembler.hh:158:16: warning: 'oxli::JunctionCountAssembler::_ksize' will be initialized after [-Wreorder] 158 | WordLength _ksize; | ^~~~~~ include/oxli/assembler.hh:153:15: warning: 'oxli::Traverser oxli::JunctionCountAssembler::traverser' [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh:153:15: warning: 'oxli::JunctionCountAssembler::traverser' will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ include/oxli/assembler.hh:151:21: warning: 'oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm' [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:626:1: required from here src/oxli/hashtable.cc:138:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 138 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:643:1: required from here src/oxli/hashtable.cc:208:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 208 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_with_mask(oxli::read_parsers::ReadParserPtr&, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:662:1: required from here src/oxli/hashtable.cc:168:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 168 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding_with_mask(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:685:1: required from here src/oxli/hashtable.cc:250:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 250 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/hllcounter.cc: In instantiation of 'void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hllcounter.cc:435:1: required from here src/oxli/hllcounter.cc:366:40: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 366 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/read_aligner.cc:48: include/oxli/read_aligner.hh:114:15: warning: 'oxli::freq_default' defined but not used [-Wunused-variable] 114 | static double freq_default[] = { log2(0.955), | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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++/13/memory:78, from third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from src/oxli/read_parsers.cc:38: /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/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++/13/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++/13/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++/13/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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61: third-party/seqan/core/include/seqan/store/store_all.h: In function 'void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)': third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 1733 | if (alignQualityStoreLengthPre == 0u) | ^~ third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/subset.cc: In member function 'size_t oxli::SubsetPartition::output_partitioned_file(const std::string&, const std::string&, bool, oxli::CallbackFn, void*)': src/oxli/subset.cc:136:24: warning: unused variable 'ksize' [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:202:5: required from here include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ src/oxli/traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:203:5: required from here include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -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 -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 creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/build creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/build/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/build/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/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/build/khmer/_oxli 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 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:744: 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:84: _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) WARNING: The wheel package is not available. /usr/lib/python3/dist-packages/setuptools/dist.py:744: 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' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'khmer.build.khmer._oxli' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'khmer.build.khmer._oxli' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'khmer.build.khmer._oxli' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'khmer.build.khmer._oxli' to be distributed and are already explicitly excluding 'khmer.build.khmer._oxli' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'khmer.build.khmer.build.khmer._oxli' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'khmer.build.khmer.build.khmer._oxli' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'khmer.build.khmer.build.khmer._oxli' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'khmer.build.khmer.build.khmer._oxli' to be distributed and are already explicitly excluding 'khmer.build.khmer.build.khmer._oxli' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/build creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/build/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/build/khmer/_oxli copying khmer/build/khmer/_oxli/oxli_exception_convert.hh -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/build/khmer/_oxli creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/build/khmer/build creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/build/khmer/build/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/build/khmer/build/khmer/_oxli copying khmer/build/khmer/build/khmer/_oxli/oxli_exception_convert.hh -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/build/khmer/build/khmer/_oxli UPDATING /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_version.py set /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_version.py to '3.0.0a3' running build_ext bash -c "cd third-party/cqf && make" make[2]: Entering directory '/build/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor 'oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)': include/oxli/assembler.hh:80:23: warning: 'oxli::LinearAssembler::graph' will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ include/oxli/assembler.hh:79:16: warning: 'oxli::WordLength oxli::LinearAssembler::_ksize' [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor 'oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()': src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type 'oxli::LinearAssembler' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh: In constructor 'oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)': include/oxli/assembler.hh:158:16: warning: 'oxli::JunctionCountAssembler::_ksize' will be initialized after [-Wreorder] 158 | WordLength _ksize; | ^~~~~~ include/oxli/assembler.hh:153:15: warning: 'oxli::Traverser oxli::JunctionCountAssembler::traverser' [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh:153:15: warning: 'oxli::JunctionCountAssembler::traverser' will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ include/oxli/assembler.hh:151:21: warning: 'oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm' [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:626:1: required from here src/oxli/hashtable.cc:138:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 138 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:643:1: required from here src/oxli/hashtable.cc:208:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 208 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_with_mask(oxli::read_parsers::ReadParserPtr&, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:662:1: required from here src/oxli/hashtable.cc:168:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 168 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding_with_mask(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:685:1: required from here src/oxli/hashtable.cc:250:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 250 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/hllcounter.cc: In instantiation of 'void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hllcounter.cc:435:1: required from here src/oxli/hllcounter.cc:366:40: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 366 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/read_aligner.cc:48: include/oxli/read_aligner.hh:114:15: warning: 'oxli::freq_default' defined but not used [-Wunused-variable] 114 | static double freq_default[] = { log2(0.955), | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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++/13/memory:78, from third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from src/oxli/read_parsers.cc:38: /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/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++/13/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++/13/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++/13/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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61: third-party/seqan/core/include/seqan/store/store_all.h: In function 'void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)': third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 1733 | if (alignQualityStoreLengthPre == 0u) | ^~ third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/storage.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/subset.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/subset.cc: In member function 'size_t oxli::SubsetPartition::output_partitioned_file(const std::string&, const std::string&, bool, oxli::CallbackFn, void*)': src/oxli/subset.cc:136:24: warning: unused variable 'ksize' [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:202:5: required from here include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ src/oxli/traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:203:5: required from here include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_khmer.cpython-311-x86_64-linux-gnu.so -fopenmp running build_scripts running install_lib creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11 creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/build_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/partition.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/kfile.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/khmer_logger.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/khmer_args.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/build creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/build/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/build/khmer/build creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/build/khmer/build/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/build/khmer/build/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/build/khmer/build/khmer/_oxli/oxli_exception_convert.hh -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/build/khmer/build/khmer/_oxli creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/build/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/build/khmer/_oxli/oxli_exception_convert.hh -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/build/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_lump.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_memory.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_oxli_functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_qfstorage.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_nibblestorage.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/.gitignore -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_subset_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_version.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_read_handling.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_sequence_validation.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_script_output.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_read_parsers.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_sandbox_scripts.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_normalize_by_median.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_scripts.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_hashset.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_banding.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_counttable.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_script_arguments.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/graph_features.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_cython_parsing.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_threaded_sequence_processor.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_hll.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_counting_single.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_countgraph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_tabletype.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_labelhash.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_cpython_hierarchy.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-output-partitions.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/100-reads.fq.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/100-reads.fq.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/badversion-k12.ht -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-reads.fq.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-slash1.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fq.pe -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/README.rst -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-error-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/simple-genome.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.malformat.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-fastq-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-impaired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fa.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/badversion-k32.tagset -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken4.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/filter-test-A.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-X2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-short.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-sweep-contigs.fp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken3.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed-witherror.fa.pe -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/empty-file.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken2.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/truncated.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-graph5.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fa.se -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/normC20k20.ct -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-large.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fa.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/real-partition-small.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/simple-genome-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed-2.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-fastq-n-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/goodversion-k32.tagset -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-labels.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-slash1.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.even.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-overlap1.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/filter-test-B.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/banding-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken4.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-overlap2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fa.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-empty.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/multi-output.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-sweep-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/bogus.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.odd.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/biglump-random-20-a.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/empty-file -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/badversion-k32.stoptags -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/fakelump.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/all-A.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/single-read.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-sweep-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-paired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-3.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/empty-file.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/badversion-k12.ct -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/dn-test-none-paired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/seq-b.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fq.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-reads.fq.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-31-c.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/casava_18-pe.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fa.pe -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-filter-abund-Ns.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken.fq.paired_bad -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-empty.fa.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-graph.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fa.part -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/unclean-reads.fastq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/real-partition-tiny.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-multi.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fa.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/branched-genome.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-2.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired_one.base.dif.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/goodversion-k12.ht -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-fastq-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed-broken.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/seq-a.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fq.se -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/readaligner-k12.json -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/readaligner-default.json -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fq.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-b.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.malformat.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/goodversion-k12.ht.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/single-read.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-graph2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/combine_parts_1.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-paired.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/goodversion-k32.stoptags -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/fakelump.fa.stoptags.txt -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-transcript.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-slash1.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken2.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/valid-read-testing.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken.fq.badright -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken.fq.badleft -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken3.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_read_aligner.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_filter_abund.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/khmer_tst_utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_assembly.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_nodegraph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/table_fixtures.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_streaming_io.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/trimming.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hllcounter.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/legacy_partitioning.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/utils.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/oxli_exception_convert.cc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashing.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/assembly.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/legacy_partitioning.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/utils.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashing.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashset.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashset.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/parsing.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/readaligner.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/parsing.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/utils.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashing.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/parsing.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/assembly.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/assembly.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/oxli_exception_convert.hh -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/labeling.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/traversal.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashset.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/graphs.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/traversal.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/oxli_types.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/readaligner.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/graphs.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/labeling.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/readaligner.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/labeling.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/graphs.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/traversal.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashset.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hllcounter.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/parsing.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hllcounter.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hllcounter.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashing.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/legacy_partitioning.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_khmer.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_version.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/thread_utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/build_graph.py to build_graph.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/partition.py to partition.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/functions.py to functions.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/kfile.py to kfile.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/khmer_logger.py to khmer_logger.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/khmer_args.py to khmer_args.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_lump.py to test_lump.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_memory.py to test_memory.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_oxli_functions.py to test_oxli_functions.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_qfstorage.py to test_qfstorage.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_nibblestorage.py to test_nibblestorage.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py to test_subset_graph.cpython-311.pyc /usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py:61: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py:82: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py:278: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py:476: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py:509: SyntaxWarning: "is" with a literal. Did you mean "=="? byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_functions.py to test_functions.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_version.py to test_version.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_read_handling.py to test_read_handling.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_sequence_validation.py to test_sequence_validation.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_script_output.py to test_script_output.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_read_parsers.py to test_read_parsers.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_sandbox_scripts.py to test_sandbox_scripts.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_normalize_by_median.py to test_normalize_by_median.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_scripts.py to test_scripts.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_hashset.py to test_hashset.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_banding.py to test_banding.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_counttable.py to test_counttable.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_script_arguments.py to test_script_arguments.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/graph_features.py to graph_features.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_cython_parsing.py to test_cython_parsing.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_threaded_sequence_processor.py to test_threaded_sequence_processor.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_hll.py to test_hll.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_counting_single.py to test_counting_single.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_countgraph.py to test_countgraph.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_tabletype.py to test_tabletype.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_labelhash.py to test_labelhash.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_cpython_hierarchy.py to test_cpython_hierarchy.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_read_aligner.py to test_read_aligner.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_filter_abund.py to test_filter_abund.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_graph.py to test_graph.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/khmer_tst_utils.py to khmer_tst_utils.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_assembly.py to test_assembly.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_nodegraph.py to test_nodegraph.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/table_fixtures.py to table_fixtures.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_streaming_io.py to test_streaming_io.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/trimming.py to trimming.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/utils.py to utils.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_version.py to _version.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/thread_utils.py to thread_utils.cpython-311.pyc running install_egg_info Copying khmer.egg-info to /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer-3.0.0a3.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.11/unique-kmers.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/count-median.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/load-into-counting.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/normalize-by-median.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/make-initial-stoptags.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/extract-paired-reads.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/sample-reads-randomly.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/abundance-dist.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/partition-graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/extract-partitions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/filter-abund.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/readstats.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/trim-low-abund.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/merge-partitions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/abundance-dist-single.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/interleave-reads.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/find-knots.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/fastq-to-fasta.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/load-graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/extract-long-sequences.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/split-paired-reads.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/do-partition.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/annotate-partitions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/filter-stoptags.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/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 3.11" 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:/i/capture/the/path ; 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 3.12.3, pytest-7.4.4, 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 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 ............................................... [ 28%] .......................................... [ 31%] tests/test_counting_single.py ......................... [ 33%] tests/test_counttable.py ..................... [ 34%] tests/test_cpython_hierarchy.py .... [ 35%] tests/test_cython_parsing.py ......................................... [ 37%] tests/test_filter_abund.py ................... [ 39%] tests/test_functions.py .................. [ 40%] tests/test_graph.py ............................ [ 42%] tests/test_hashset.py .............. [ 43%] tests/test_hll.py ......................... [ 45%] tests/test_labelhash.py ...................... [ 46%] tests/test_lump.py ...... [ 47%] tests/test_memory.py ........ [ 47%] tests/test_nibblestorage.py ..... [ 48%] tests/test_nodegraph.py ................................................ [ 51%] .................... [ 52%] tests/test_normalize_by_median.py ...................................... [ 55%] [ 55%] tests/test_oxli_functions.py .... [ 55%] tests/test_qfstorage.py . [ 55%] tests/test_read_aligner.py ................ [ 56%] tests/test_read_handling.py ................................ [ 59%] tests/test_read_parsers.py .............................. [ 61%] tests/test_sandbox_scripts.py ssssssssssssssssss [ 62%] tests/test_script_arguments.py ............................. [ 64%] tests/test_script_output.py ........... [ 65%] tests/test_scripts.py .................................................. [ 68%] ........................................................................ [ 73%] ........................ [ 75%] tests/test_sequence_validation.py ...................................... [ 77%] ............. [ 78%] tests/test_streaming_io.py ............................ [ 80%] tests/test_subset_graph.py ........................... [ 82%] tests/test_tabletype.py ................................................ [ 85%] ..s.s.ss................................................................ [ 90%] ........................................................................ [ 95%] ..................................................... [ 99%] tests/test_threaded_sequence_processor.py ...... [ 99%] tests/test_version.py . [100%] ==== 1422 passed, 22 skipped, 47 deselected, 1 xpassed in 118.91s (0:01:58) ==== 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:/i/capture/the/path ; cd '/build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build'; export PYTHONPATH=/build/reproducible-path/khmer-3.0.0~a3+dfsg; python3.11 -m pytest -m 'not known_failing and not jenkins and not huge and not noroot' -q ============================= test session starts ============================== platform linux -- Python 3.11.9, pytest-7.4.4, pluggy-1.5.0 rootdir: /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build configfile: pytest.ini testpaths: tests collected 1492 items / 47 deselected / 1445 selected tests/test_assembly.py ................................................. [ 3%] ........................................................................ [ 8%] ........................................................................ [ 13%] ........................................................................ [ 18%] ........................................................................ [ 23%] .................... [ 24%] tests/test_banding.py ............ [ 25%] tests/test_countgraph.py ............................................... [ 28%] .......................................... [ 31%] tests/test_counting_single.py ......................... [ 33%] tests/test_counttable.py ..................... [ 34%] tests/test_cpython_hierarchy.py .... [ 35%] tests/test_cython_parsing.py ......................................... [ 37%] tests/test_filter_abund.py ................... [ 39%] tests/test_functions.py .................. [ 40%] tests/test_graph.py ............................ [ 42%] tests/test_hashset.py .............. [ 43%] tests/test_hll.py ......................... [ 45%] tests/test_labelhash.py ...................... [ 46%] tests/test_lump.py ...... [ 47%] tests/test_memory.py ........ [ 47%] tests/test_nibblestorage.py ..... [ 48%] tests/test_nodegraph.py ................................................ [ 51%] .................... [ 52%] tests/test_normalize_by_median.py ...................................... [ 55%] [ 55%] tests/test_oxli_functions.py .... [ 55%] tests/test_qfstorage.py . [ 55%] tests/test_read_aligner.py ................ [ 56%] tests/test_read_handling.py ................................ [ 59%] tests/test_read_parsers.py .............................. [ 61%] tests/test_sandbox_scripts.py ssssssssssssssssss [ 62%] tests/test_script_arguments.py ............................. [ 64%] tests/test_script_output.py ........... [ 65%] tests/test_scripts.py .................................................. [ 68%] ........................................................................ [ 73%] ........................ [ 75%] tests/test_sequence_validation.py ...................................... [ 77%] ............. [ 78%] tests/test_streaming_io.py ............................ [ 80%] tests/test_subset_graph.py ........................... [ 82%] tests/test_tabletype.py ................................................ [ 85%] ..s.s.ss................................................................ [ 90%] ........................................................................ [ 95%] ..................................................... [ 99%] tests/test_threaded_sequence_processor.py ...... [ 99%] tests/test_version.py . [100%] ========= 1423 passed, 22 skipped, 47 deselected in 144.43s (0:02:24) ========== rm -fr -- /tmp/dh-xdg-rundir-7ic_QbWA make[1]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild rm -f -- debian/khmer-common.substvars debian/khmer.substvars debian/liboxli1.substvars debian/liboxli-dev.substvars rm -fr -- debian/.debhelper/generated/khmer-common/ debian/khmer-common/ debian/tmp/ debian/.debhelper/generated/khmer/ debian/khmer/ debian/.debhelper/generated/liboxli1/ debian/liboxli1/ debian/.debhelper/generated/liboxli-dev/ debian/liboxli-dev/ dh_auto_install -O--buildsystem=pybuild install -m0755 -d /build/reproducible-path/khmer-3.0.0\~a3\+dfsg/debian/tmp pybuild --install -i python{version} -p "3.12 3.11" --dest-dir /build/reproducible-path/khmer-3.0.0\~a3\+dfsg/debian/tmp I: pybuild base:311: /usr/bin/python3.12 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:744: 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:84: _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) WARNING: The wheel package is not available. /usr/lib/python3/dist-packages/setuptools/dist.py:744: 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' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'khmer.build.khmer._oxli' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'khmer.build.khmer._oxli' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'khmer.build.khmer._oxli' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'khmer.build.khmer._oxli' to be distributed and are already explicitly excluding 'khmer.build.khmer._oxli' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'khmer.build.khmer.build.khmer._oxli' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'khmer.build.khmer.build.khmer._oxli' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'khmer.build.khmer.build.khmer._oxli' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'khmer.build.khmer.build.khmer._oxli' to be distributed and are already explicitly excluding 'khmer.build.khmer.build.khmer._oxli' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/build/khmer/build creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/build/khmer/build/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/build/khmer/build/khmer/_oxli copying khmer/build/khmer/build/khmer/_oxli/oxli_exception_convert.hh -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/build/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[1]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' building 'khmer._khmer' extension x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor 'oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)': include/oxli/assembler.hh:80:23: warning: 'oxli::LinearAssembler::graph' will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ include/oxli/assembler.hh:79:16: warning: 'oxli::WordLength oxli::LinearAssembler::_ksize' [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor 'oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()': src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type 'oxli::LinearAssembler' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh: In constructor 'oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)': include/oxli/assembler.hh:158:16: warning: 'oxli::JunctionCountAssembler::_ksize' will be initialized after [-Wreorder] 158 | WordLength _ksize; | ^~~~~~ include/oxli/assembler.hh:153:15: warning: 'oxli::Traverser oxli::JunctionCountAssembler::traverser' [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh:153:15: warning: 'oxli::JunctionCountAssembler::traverser' will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ include/oxli/assembler.hh:151:21: warning: 'oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm' [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:626:1: required from here src/oxli/hashtable.cc:138:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 138 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:643:1: required from here src/oxli/hashtable.cc:208:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 208 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_with_mask(oxli::read_parsers::ReadParserPtr&, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:662:1: required from here src/oxli/hashtable.cc:168:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 168 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding_with_mask(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:685:1: required from here src/oxli/hashtable.cc:250:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 250 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/hllcounter.cc: In instantiation of 'void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hllcounter.cc:435:1: required from here src/oxli/hllcounter.cc:366:40: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 366 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/read_aligner.cc:48: include/oxli/read_aligner.hh:114:15: warning: 'oxli::freq_default' defined but not used [-Wunused-variable] 114 | static double freq_default[] = { log2(0.955), | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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++/13/memory:78, from third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from src/oxli/read_parsers.cc:38: /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/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++/13/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++/13/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++/13/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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61: third-party/seqan/core/include/seqan/store/store_all.h: In function 'void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)': third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 1733 | if (alignQualityStoreLengthPre == 0u) | ^~ third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/subset.cc: In member function 'size_t oxli::SubsetPartition::output_partitioned_file(const std::string&, const std::string&, bool, oxli::CallbackFn, void*)': src/oxli/subset.cc:136:24: warning: unused variable 'ksize' [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:202:5: required from here include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ src/oxli/traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:203:5: required from here include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -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 -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/.pytest_cache copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/.pytest_cache/.gitignore -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/.pytest_cache copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/.pytest_cache/README.md -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/.pytest_cache copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/.pytest_cache/CACHEDIR.TAG -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/.pytest_cache creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/.pytest_cache/v creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/.pytest_cache/v/cache copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/.pytest_cache/v/cache/stepwise -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/.pytest_cache/v/cache copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/.pytest_cache/v/cache/nodeids -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/.pytest_cache/v/cache 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 creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli/__pycache__/build_graph.cpython-312.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli/__pycache__/partition.cpython-312.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli/__pycache__/functions.cpython-312.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/oxli/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/oxli/__pycache__ 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 creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/__pycache__/thread_utils.cpython-312.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/__pycache__/trimming.cpython-312.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/__pycache__/_version.cpython-312.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/__pycache__/kfile.cpython-312.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/__pycache__/khmer_args.cpython-312.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/__pycache__/utils.cpython-312.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/__pycache__/khmer_logger.cpython-312.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/__pycache__ 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 creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/build creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/build/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/build/khmer/build creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/build/khmer/build/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/build/khmer/build/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/build/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/build/khmer/build/khmer/_oxli creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/build/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/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/build/khmer/_oxli 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 creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.12_khmer/build/khmer/_oxli/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.12/dist-packages/khmer/_oxli/__pycache__ 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 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:744: 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:84: _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) WARNING: The wheel package is not available. /usr/lib/python3/dist-packages/setuptools/dist.py:744: 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' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'khmer.build.khmer._oxli' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'khmer.build.khmer._oxli' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'khmer.build.khmer._oxli' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'khmer.build.khmer._oxli' to be distributed and are already explicitly excluding 'khmer.build.khmer._oxli' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'khmer.build.khmer.build.khmer._oxli' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'khmer.build.khmer.build.khmer._oxli' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'khmer.build.khmer.build.khmer._oxli' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'khmer.build.khmer.build.khmer._oxli' to be distributed and are already explicitly excluding 'khmer.build.khmer.build.khmer._oxli' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'khmer.build.khmer.build.khmer.build.khmer._oxli' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'khmer.build.khmer.build.khmer.build.khmer._oxli' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'khmer.build.khmer.build.khmer.build.khmer._oxli' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'khmer.build.khmer.build.khmer.build.khmer._oxli' to be distributed and are already explicitly excluding 'khmer.build.khmer.build.khmer.build.khmer._oxli' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/build/khmer/build/khmer/build creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/build/khmer/build/khmer/build/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/build/khmer/build/khmer/build/khmer/_oxli copying khmer/build/khmer/build/khmer/build/khmer/_oxli/oxli_exception_convert.hh -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/build/khmer/build/khmer/build/khmer/_oxli UPDATING /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_version.py set /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_version.py to '3.0.0a3' running build_ext bash -c "cd third-party/cqf && make" make[1]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/third-party/cqf' building 'khmer._khmer' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor 'oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)': include/oxli/assembler.hh:80:23: warning: 'oxli::LinearAssembler::graph' will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ include/oxli/assembler.hh:79:16: warning: 'oxli::WordLength oxli::LinearAssembler::_ksize' [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor 'oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()': src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type 'oxli::LinearAssembler' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh: In constructor 'oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)': include/oxli/assembler.hh:158:16: warning: 'oxli::JunctionCountAssembler::_ksize' will be initialized after [-Wreorder] 158 | WordLength _ksize; | ^~~~~~ include/oxli/assembler.hh:153:15: warning: 'oxli::Traverser oxli::JunctionCountAssembler::traverser' [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ include/oxli/assembler.hh:153:15: warning: 'oxli::JunctionCountAssembler::traverser' will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ include/oxli/assembler.hh:151:21: warning: 'oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm' [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:626:1: required from here src/oxli/hashtable.cc:138:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 138 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:643:1: required from here src/oxli/hashtable.cc:208:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 208 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_with_mask(oxli::read_parsers::ReadParserPtr&, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:662:1: required from here src/oxli/hashtable.cc:168:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 168 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of 'void oxli::Hashtable::consume_seqfile_banding_with_mask(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, oxli::Hashtable*, unsigned int, unsigned int&, long long unsigned int&, bool) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hashtable.cc:685:1: required from here src/oxli/hashtable.cc:250:18: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 250 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/hllcounter.cc: In instantiation of 'void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::shared_ptr >]': src/oxli/hllcounter.cc:435:1: required from here src/oxli/hllcounter.cc:366:40: warning: catching polymorphic type 'struct oxli::read_parsers::NoMoreReadsAvailable' by value [-Wcatch-value=] 366 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/read_aligner.cc:48: include/oxli/read_aligner.hh:114:15: warning: 'oxli::freq_default' defined but not used [-Wunused-variable] 114 | static double freq_default[] = { log2(0.955), | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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++/13/memory:78, from third-party/seqan/core/include/seqan/basic/test_system.h:53: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from src/oxli/read_parsers.cc:38: /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/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++/13/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++/13/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++/13/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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here 65 | 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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61: third-party/seqan/core/include/seqan/store/store_all.h: In function 'void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&)': third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 1733 | if (alignQualityStoreLengthPre == 0u) | ^~ third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/storage.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/subset.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/oxli/subset.cc: In member function 'size_t oxli::SubsetPartition::output_partitioned_file(const std::string&, const std::string&, bool, oxli::CallbackFn, void*)': src/oxli/subset.cc:136:24: warning: unused variable 'ksize' [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:202:5: required from here include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ src/oxli/traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:203:5: required from here include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/usr/include/python3.11 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -fopenmp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-cpython-311/src/khmer/_cpy_utils.o build/temp.linux-x86_64-cpython-311/src/oxli/alphabets.o build/temp.linux-x86_64-cpython-311/src/oxli/assembler.o build/temp.linux-x86_64-cpython-311/src/oxli/hashgraph.o build/temp.linux-x86_64-cpython-311/src/oxli/hashtable.o build/temp.linux-x86_64-cpython-311/src/oxli/hllcounter.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_filters.o build/temp.linux-x86_64-cpython-311/src/oxli/kmer_hash.o build/temp.linux-x86_64-cpython-311/src/oxli/labelhash.o build/temp.linux-x86_64-cpython-311/src/oxli/read_aligner.o build/temp.linux-x86_64-cpython-311/src/oxli/read_parsers.o build/temp.linux-x86_64-cpython-311/src/oxli/storage.o build/temp.linux-x86_64-cpython-311/src/oxli/subset.o build/temp.linux-x86_64-cpython-311/src/oxli/traversal.o build/temp.linux-x86_64-cpython-311/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_khmer.cpython-311-x86_64-linux-gnu.so -fopenmp running build_scripts running install_lib creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11 creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/.pytest_cache copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/.pytest_cache/.gitignore -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/.pytest_cache copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/.pytest_cache/README.md -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/.pytest_cache copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/.pytest_cache/CACHEDIR.TAG -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/.pytest_cache creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/.pytest_cache/v creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/.pytest_cache/v/cache copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/.pytest_cache/v/cache/stepwise -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/.pytest_cache/v/cache copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/.pytest_cache/v/cache/nodeids -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/.pytest_cache/v/cache creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/build_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/__pycache__/functions.cpython-311.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/__pycache__/partition.cpython-311.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/__pycache__/build_graph.cpython-311.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/partition.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/oxli/functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/kfile.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/__pycache__/utils.cpython-311.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/__pycache__/thread_utils.cpython-311.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/__pycache__/khmer_args.cpython-311.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/__pycache__/khmer_logger.cpython-311.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/__pycache__/trimming.cpython-311.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/__pycache__/_version.cpython-311.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/__pycache__/kfile.cpython-311.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/khmer_logger.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/khmer_args.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/build creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/build/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/build/khmer/build creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/build/khmer/build/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/build/khmer/build/khmer/build creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/build/khmer/build/khmer/build/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/build/khmer/build/khmer/build/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/build/khmer/build/khmer/build/khmer/_oxli/oxli_exception_convert.hh -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/build/khmer/build/khmer/build/khmer/_oxli creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/build/khmer/build/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/build/khmer/build/khmer/_oxli/oxli_exception_convert.hh -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/build/khmer/build/khmer/_oxli creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/build/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/build/khmer/_oxli/oxli_exception_convert.hh -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/build/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_lump.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_memory.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_oxli_functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_qfstorage.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_nibblestorage.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/.gitignore -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_subset_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_functions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_version.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_read_handling.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_sequence_validation.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_script_output.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_read_parsers.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_sandbox_scripts.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_normalize_by_median.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_scripts.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_hashset.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_banding.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_counttable.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_script_arguments.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/graph_features.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_cython_parsing.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_threaded_sequence_processor.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_hll.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_counting_single.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_countgraph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_tabletype.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_labelhash.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_cpython_hierarchy.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-output-partitions.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/100-reads.fq.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/100-reads.fq.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/badversion-k12.ht -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-reads.fq.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-slash1.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fq.pe -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/README.rst -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-error-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/simple-genome.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.malformat.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-fastq-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-impaired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fa.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/badversion-k32.tagset -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken4.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/filter-test-A.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-X2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-short.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-sweep-contigs.fp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken3.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed-witherror.fa.pe -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/empty-file.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken2.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/truncated.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-graph5.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fa.se -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/normC20k20.ct -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-large.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fa.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/real-partition-small.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/simple-genome-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed-2.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-fastq-n-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/goodversion-k32.tagset -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-labels.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-slash1.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.even.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-overlap1.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/filter-test-B.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/banding-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken4.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-overlap2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fa.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-empty.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/multi-output.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-sweep-reads.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/bogus.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.odd.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/biglump-random-20-a.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/empty-file -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/badversion-k32.stoptags -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/fakelump.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/all-A.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/single-read.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-sweep-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-paired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-3.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/empty-file.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/badversion-k12.ct -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/dn-test-none-paired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/seq-b.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fq.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-reads.fq.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-31-c.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/casava_18-pe.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fa.pe -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-filter-abund-Ns.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken.fq.paired_bad -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-empty.fa.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-graph.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fa.part -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/unclean-reads.fastq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/real-partition-tiny.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-multi.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fa.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/branched-genome.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-2.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired_one.base.dif.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/goodversion-k12.ht -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-fastq-reads.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed-broken.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/seq-a.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-mixed.fq.se -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/readaligner-k12.json -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/readaligner-default.json -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fq.bz2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-b.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/random-20-a.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.malformat.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/goodversion-k12.ht.gz -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/single-read.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-graph2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/combine_parts_1.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-paired.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/goodversion-k32.stoptags -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_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/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/fakelump.fa.stoptags.txt -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-transcript.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-slash1.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken2.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/valid-read-testing.fq -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/test-abund-read-2.fa -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken.fq.badright -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken.fq.badleft -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken3.fq.1 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test-data/paired-broken.fq.2 -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test-data copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_read_aligner.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_filter_abund.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/khmer_tst_utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_assembly.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_nodegraph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/table_fixtures.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/tests/test_streaming_io.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/trimming.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hllcounter.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/legacy_partitioning.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/utils.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli creating /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli/__pycache__ copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/oxli_exception_convert.cc -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashing.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/assembly.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/legacy_partitioning.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/utils.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashing.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashset.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashset.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/parsing.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/readaligner.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/parsing.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/utils.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/__init__.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashing.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/parsing.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/assembly.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/assembly.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/oxli_exception_convert.hh -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/labeling.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/traversal.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashset.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/graphs.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/traversal.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/oxli_types.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/readaligner.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/graphs.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/labeling.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/readaligner.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/labeling.cpp -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/graphs.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/traversal.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashset.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hllcounter.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/parsing.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hllcounter.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hllcounter.pyx -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/hashing.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_oxli/legacy_partitioning.pxd -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_khmer.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/_version.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer copying /build/reproducible-path/khmer-3.0.0~a3+dfsg/.pybuild/cpython3_3.11_khmer/build/khmer/thread_utils.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/build_graph.py to build_graph.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/partition.py to partition.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/oxli/functions.py to functions.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/kfile.py to kfile.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/khmer_logger.py to khmer_logger.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/khmer_args.py to khmer_args.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_lump.py to test_lump.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_memory.py to test_memory.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_oxli_functions.py to test_oxli_functions.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_qfstorage.py to test_qfstorage.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_nibblestorage.py to test_nibblestorage.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py to test_subset_graph.cpython-311.pyc /usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py:61: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py:82: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py:278: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py:476: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.11/dist-packages/khmer/tests/test_subset_graph.py:509: SyntaxWarning: "is" with a literal. Did you mean "=="? byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_functions.py to test_functions.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_version.py to test_version.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_read_handling.py to test_read_handling.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_sequence_validation.py to test_sequence_validation.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_script_output.py to test_script_output.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_read_parsers.py to test_read_parsers.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_sandbox_scripts.py to test_sandbox_scripts.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_normalize_by_median.py to test_normalize_by_median.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_scripts.py to test_scripts.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_hashset.py to test_hashset.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_banding.py to test_banding.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_counttable.py to test_counttable.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_script_arguments.py to test_script_arguments.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/graph_features.py to graph_features.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_cython_parsing.py to test_cython_parsing.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_threaded_sequence_processor.py to test_threaded_sequence_processor.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_hll.py to test_hll.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_counting_single.py to test_counting_single.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_countgraph.py to test_countgraph.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_tabletype.py to test_tabletype.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_labelhash.py to test_labelhash.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_cpython_hierarchy.py to test_cpython_hierarchy.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_read_aligner.py to test_read_aligner.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_filter_abund.py to test_filter_abund.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_graph.py to test_graph.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/khmer_tst_utils.py to khmer_tst_utils.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_assembly.py to test_assembly.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_nodegraph.py to test_nodegraph.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/table_fixtures.py to table_fixtures.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/tests/test_streaming_io.py to test_streaming_io.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/trimming.py to trimming.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/utils.py to utils.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_oxli/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/_version.py to _version.cpython-311.pyc byte-compiling /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer/thread_utils.py to thread_utils.cpython-311.pyc running install_egg_info Copying khmer.egg-info to /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/python3.11/dist-packages/khmer-3.0.0a3.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.11/unique-kmers.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/count-median.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/load-into-counting.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/normalize-by-median.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/make-initial-stoptags.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/extract-paired-reads.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/sample-reads-randomly.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/abundance-dist.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/partition-graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/extract-partitions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/filter-abund.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/readstats.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/trim-low-abund.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/merge-partitions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/abundance-dist-single.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/interleave-reads.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/find-knots.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/fastq-to-fasta.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/load-graph.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/extract-long-sequences.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/split-paired-reads.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/do-partition.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/annotate-partitions.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/filter-stoptags.py -> /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.11/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 rm -f debian/khmer-common.debhelper.log debian/khmer.debhelper.log debian/liboxli-dev.debhelper.log debian/liboxli1.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg' cd src/oxli && /usr/bin/make PREFIX=../debian/tmp install make[2]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/src/oxli' rm -rf ../debian/tmp/include/oxli ../debian/tmp/include/khmer mkdir -p ../debian/tmp/lib ../debian/tmp/lib/pkgconfig ../debian/tmp/include/oxli cp -r ../../include/oxli/hashtable.hh ../../include/oxli/hashgraph.hh ../../include/oxli/hllcounter.hh ../../include/oxli/oxli_exception.hh ../../include/oxli/oxli.hh ../../include/oxli/kmer_hash.hh ../../include/oxli/labelhash.hh ../../include/oxli/traversal.hh ../../include/oxli/read_aligner.hh ../../include/oxli/read_parsers.hh ../../include/oxli/subset.hh ../../include/oxli/kmer_filters.hh ../../include/oxli/assembler.hh ../../include/oxli/alphabets.hh ../../include/oxli/storage.hh \ ../../third-party/smhasher/MurmurHash3.h \ ../debian/tmp/include/oxli/ cp oxli.pc ../debian/tmp/lib/pkgconfig/ cp liboxli.so.1 liboxli.a ../debian/tmp/lib/ ln -sf ../debian/tmp/lib/liboxli.so.1 ../debian/tmp/lib/liboxli.so make[2]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg/src/oxli' dh_install install -m0755 -d debian/khmer-common/usr/share/file/khmer cp --reflink=auto -a ./include/oxli/magic debian/khmer-common/usr/share/file/khmer/ install -m0755 -d debian/khmer//usr/share/metainfo/ cp --reflink=auto -a ./debian/khmer.metainfo.xml debian/khmer//usr/share/metainfo// install -m0755 -d debian/khmer/usr/bin/ cp --reflink=auto -a ./debian/bin/khmer debian/khmer/usr/bin// install -m0755 -d debian/liboxli1/usr/lib/x86_64-linux-gnu cp --reflink=auto -a ./src/oxli/liboxli.so.1 debian/liboxli1/usr/lib/x86_64-linux-gnu/ install -m0755 -d debian/liboxli-dev/usr/include/oxli cp --reflink=auto -a ./include/oxli/alphabets.hh ./include/oxli/assembler.hh ./include/oxli/hashgraph.hh ./include/oxli/hashtable.hh ./include/oxli/hllcounter.hh ./include/oxli/kmer_filters.hh ./include/oxli/kmer_hash.hh ./include/oxli/labelhash.hh ./include/oxli/oxli.hh ./include/oxli/oxli_exception.hh ./include/oxli/read_aligner.hh ./include/oxli/read_parsers.hh ./include/oxli/storage.hh ./include/oxli/subset.hh ./include/oxli/traversal.hh debian/liboxli-dev/usr/include/oxli/ install -m0755 -d debian/liboxli-dev/usr/include/oxli/smhasher cp --reflink=auto -a ./third-party/smhasher/MurmurHash3.h debian/liboxli-dev/usr/include/oxli/smhasher/ install -m0755 -d debian/liboxli-dev/usr/lib/x86_64-linux-gnu cp --reflink=auto -a ./src/oxli/liboxli.a ./src/oxli/liboxli.so debian/liboxli-dev/usr/lib/x86_64-linux-gnu/ install -m0755 -d debian/liboxli-dev/usr/lib/x86_64-linux-gnu/pkgconfig cp --reflink=auto -a ./src/oxli/oxli.pc debian/liboxli-dev/usr/lib/x86_64-linux-gnu/pkgconfig/ find debian/khmer -name .gitignore -delete make[1]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg' dh_installdocs -O--buildsystem=pybuild install -m0755 -d debian/khmer-common/usr/share/doc/khmer-common install -m0755 -d debian/khmer-common/usr/share/doc/khmer-common cd './build/sphinx/html/..' && find 'html' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/khmer-3.0.0~a3+dfsg/debian/khmer-common/usr/share/doc/khmer-common cp --reflink=auto -a ./CITATION debian/khmer-common/usr/share/doc/khmer-common cp --reflink=auto -a ./README.rst debian/khmer-common/usr/share/doc/khmer-common cp --reflink=auto -a ./debian/README.test debian/khmer-common/usr/share/doc/khmer-common cp --reflink=auto -a ./debian/tests/run-unit-test debian/khmer-common/usr/share/doc/khmer-common cp --reflink=auto -a ./src/oxli/test-compile.cc debian/khmer-common/usr/share/doc/khmer-common chmod -R u\+rw,go=rX debian/khmer-common/usr/share/doc install -p -m0644 debian/copyright debian/khmer-common/usr/share/doc/khmer-common/copyright install -m0755 -d debian/khmer-common/usr/share/doc-base/ install -p -m0644 debian/doc-base debian/khmer-common/usr/share/doc-base/khmer-common.khmer install -m0755 -d debian/khmer/usr/share/doc/khmer install -p -m0644 debian/copyright debian/khmer/usr/share/doc/khmer/copyright install -m0755 -d debian/liboxli1/usr/share/doc/liboxli1 install -p -m0644 debian/copyright debian/liboxli1/usr/share/doc/liboxli1/copyright install -m0755 -d debian/liboxli-dev/usr/share/doc/liboxli-dev install -p -m0644 debian/copyright debian/liboxli-dev/usr/share/doc/liboxli-dev/copyright rm -f debian/khmer-common.debhelper.log debian/khmer.debhelper.log debian/liboxli-dev.debhelper.log debian/liboxli1.debhelper.log debian/rules override_dh_sphinxdoc make[1]: Entering directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg' dh_sphinxdoc ln -sf ../../../../javascript/jquery/jquery.min.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js ln -sf ../../../../javascript/sphinxdoc/1.0/doctools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js ln -sf ../../../../javascript/sphinxdoc/1.0/language_data.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js ln -sf ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/khmer-common/usr/share/doc/khmer-common/html/_static/labibi.js ln -sf ../../../../javascript/jquery/jquery.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.js ln -sf ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js rm -rf debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees rm -f debian/khmer-common/usr/share/doc/khmer-common/html/.buildinfo mv debian/khmer-common.substvars.new debian/khmer-common.substvars mv debian/khmer-common.substvars.new debian/khmer-common.substvars mv debian/khmer-common.substvars.new debian/khmer-common.substvars mv debian/khmer-common.substvars.new debian/khmer-common.substvars mv debian/khmer-common.substvars.new debian/khmer-common.substvars rdfind -makesymlinks true -followsymlinks true\ /usr/lib/python3/dist-packages/guzzle_sphinx_theme \ debian/khmer-common debian/khmer-common/usr debian/khmer-common/usr/share debian/khmer-common/usr/share/doc-base debian/khmer-common/usr/share/doc-base/khmer-common.khmer debian/khmer-common/usr/share/doc debian/khmer-common/usr/share/doc/khmer-common debian/khmer-common/usr/share/doc/khmer-common/README.rst debian/khmer-common/usr/share/doc/khmer-common/html debian/khmer-common/usr/share/doc/khmer-common/html/searchindex.js 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debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/galaxy.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/biblio.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/scripts.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/index.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/choosing-table-sizes.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/partitioning-big-data.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/known-issues.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/install.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/guide.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/api-examples.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/blog-posts.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/examples.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/getting-help.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/user debian/khmer-common/usr/share/doc/khmer-common/html/user/scripts.html debian/khmer-common/usr/share/doc/khmer-common/html/user/blog-posts.html debian/khmer-common/usr/share/doc/khmer-common/html/user/install.html debian/khmer-common/usr/share/doc/khmer-common/html/user/guide.html debian/khmer-common/usr/share/doc/khmer-common/html/user/biblio.html debian/khmer-common/usr/share/doc/khmer-common/html/user/galaxy.html debian/khmer-common/usr/share/doc/khmer-common/html/user/partitioning-big-data.html debian/khmer-common/usr/share/doc/khmer-common/html/user/examples.html debian/khmer-common/usr/share/doc/khmer-common/html/user/api-examples.html debian/khmer-common/usr/share/doc/khmer-common/html/user/known-issues.html debian/khmer-common/usr/share/doc/khmer-common/html/user/choosing-table-sizes.html debian/khmer-common/usr/share/doc/khmer-common/html/user/getting-help.html debian/khmer-common/usr/share/doc/khmer-common/html/user/index.html debian/khmer-common/usr/share/doc/khmer-common/html/index.html debian/khmer-common/usr/share/doc/khmer-common/html/contributors.html debian/khmer-common/usr/share/doc/khmer-common/README.test debian/khmer-common/usr/share/doc/khmer-common/test-compile.cc debian/khmer-common/usr/share/doc/khmer-common/copyright debian/khmer-common/usr/share/doc/khmer-common/run-unit-test debian/khmer-common/usr/share/file debian/khmer-common/usr/share/file/khmer debian/khmer-common/usr/share/file/khmer/magic Now scanning "/usr/lib/python3/dist-packages/guzzle_sphinx_theme", found 117 files. Now scanning "debian/khmer-common"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.min.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.min.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js , found 194 files. Now scanning "debian/khmer-common/usr"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.min.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.min.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js , found 194 files. Now scanning "debian/khmer-common/usr/share"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.min.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.min.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js , found 194 files. Now scanning "debian/khmer-common/usr/share/doc-base", found 1 files. Now scanning "debian/khmer-common/usr/share/doc-base/khmer-common.khmer", found 1 files. Now scanning "debian/khmer-common/usr/share/doc"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.min.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.min.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js , found 192 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.min.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.min.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js , found 192 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/README.rst", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.min.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.min.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js , found 186 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/searchindex.js", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/LICENSE.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/search.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/genindex.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/objects.inv", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev", found 13 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/development.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/getting-started.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/binary-file-formats.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/scripts-and-sandbox.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/guidelines-continued-dev.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/release.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/hackathon.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/a-quick-guide-to-testing.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/CODE_OF_CONDUCT.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/codebase-guide.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/index.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/for-khmer-developers.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/python-api.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/contributors.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/LICENSE.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/introduction.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/dev", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/dev/python-api.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/dev/codebase-guide.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/dev/guidelines-continued-dev.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/dev/binary-file-formats.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/dev/scripts-and-sandbox.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/dev/hackathon.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/dev/index.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/dev/CODE_OF_CONDUCT.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/dev/for-khmer-developers.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/dev/a-quick-guide-to-testing.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/dev/getting-started.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/dev/development.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/dev/release.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/release-notes", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/release-notes/release-1.4.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/release-notes/release-1.2.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/release-notes/release-1.3.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/release-notes/release-1.1.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/release-notes/index.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/release-notes/release-1.0.1.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/release-notes/release-2.1.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/release-notes/release-2.0.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/release-notes/release-1.0.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/index.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/roadmap.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/environment.pickle", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/user", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/user/partitioning-big-data.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/user/biblio.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/user/getting-help.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/user/install.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/user/choosing-table-sizes.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/user/examples.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/user/index.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/user/api-examples.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/user/known-issues.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/user/scripts.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/user/galaxy.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/user/blog-posts.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.doctrees/user/guide.doctree", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes", found 9 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.3.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.2.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.0.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-2.1.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.0.1.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.1.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.4.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-2.0.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/index.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/introduction.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.buildinfo", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.min.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.min.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js , found 98 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/labibi.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js , found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/css", found 3 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/font-face.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/bootstrap.min.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/bootstrap-theme.min.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/guzzle.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js , found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts", found 84 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSans-Regular.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans", found 41 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts", found 40 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/stylesheet.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSerif-Regular.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSans-Italic.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro", found 35 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF", found 12 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF", found 6 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Light.ttf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Regular.ttf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Bold.ttf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-ExtraLight.ttf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Black.ttf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Semibold.ttf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF", found 6 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Light.otf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Bold.otf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Black.otf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Semibold.otf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-ExtraLight.otf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Regular.otf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/ReadMe.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF", found 6 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Regular.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Bold.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-ExtraLight.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Semibold.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Black.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Light.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/README.md", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/bower.json", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT", found 6 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Regular.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-ExtraLight.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Bold.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Semibold.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Light.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Black.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/SourceSerifProReadMe.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/source-serif-pro.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF", found 6 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Black.otf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Bold.otf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Regular.otf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Light.otf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Semibold.otf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-ExtraLight.otf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.woff2", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/basic.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/documentation_options.js", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//sphinx_highlight.js , found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js , found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.min.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.min.js , found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/plus.png", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js , found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/js", found 2 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.js", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.min.js", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/file.png", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/minus.png", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/pygments.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/labibi.js", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_images", found 2 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_images/artifact-removal.png", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_images/partitioning-workflow.png", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/roadmap.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources", found 41 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/LICENSE.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/index.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev", found 13 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/index.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/getting-started.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/python-api.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/scripts-and-sandbox.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/hackathon.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/development.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/codebase-guide.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/binary-file-formats.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/release.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/for-khmer-developers.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/CODE_OF_CONDUCT.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/guidelines-continued-dev.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/a-quick-guide-to-testing.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes", found 9 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.4.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/index.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.0.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.2.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-2.0.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.0.1.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-2.1.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.1.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.3.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/contributors.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/introduction.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/roadmap.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user", found 13 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/galaxy.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/biblio.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/scripts.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/index.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/choosing-table-sizes.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/partitioning-big-data.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/known-issues.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/install.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/guide.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/api-examples.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/blog-posts.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/examples.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/getting-help.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user", found 13 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/scripts.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/blog-posts.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/install.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/guide.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/biblio.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/galaxy.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/partitioning-big-data.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/examples.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/api-examples.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/known-issues.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/choosing-table-sizes.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/getting-help.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/index.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/index.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/contributors.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/README.test", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/test-compile.cc", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/copyright", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/run-unit-test", found 1 files. Now scanning "debian/khmer-common/usr/share/file", found 1 files. Now scanning "debian/khmer-common/usr/share/file/khmer", found 1 files. Now scanning "debian/khmer-common/usr/share/file/khmer/magic", found 1 files. Now have 1921 files in total. Removed 1624 files due to nonunique device and inode. Total size is 13311072 bytes or 13 MiB Removed 112 files due to unique sizes from list. 185 files left. Now eliminating candidates based on first bytes: removed 5 files from list. 180 files left. Now eliminating candidates based on last bytes: removed 0 files from list. 180 files left. Now eliminating candidates based on sha1 checksum: removed 0 files from list. 180 files left. It seems like you have 180 files that are not unique Totally, 5 MiB can be reduced. Now making results file results.txt Now making symbolic links. creating Making 90 links. if [ -f debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt ]; then \ rm debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt && \ cd debian/khmer-common/usr/share/doc/khmer-common/html/_sources/ && \ ln -s ../../CITATION citations.rst.txt; fi make[1]: Leaving directory '/build/reproducible-path/khmer-3.0.0~a3+dfsg' dh_installchangelogs -O--buildsystem=pybuild install -m0755 -d debian/liboxli-dev/usr/share/doc/liboxli-dev install -p -m0644 debian/.debhelper/generated/liboxli-dev/dh_installchangelogs.dch.trimmed debian/liboxli-dev/usr/share/doc/liboxli-dev/changelog.Debian install -p -m0644 ./CHANGELOG.md debian/liboxli-dev/usr/share/doc/liboxli-dev/changelog install -m0755 -d debian/khmer/usr/share/doc/khmer install -p -m0644 debian/.debhelper/generated/khmer/dh_installchangelogs.dch.trimmed debian/khmer/usr/share/doc/khmer/changelog.Debian install -p -m0644 ./CHANGELOG.md debian/khmer/usr/share/doc/khmer/changelog install -m0755 -d debian/khmer-common/usr/share/doc/khmer-common install -p -m0644 debian/.debhelper/generated/khmer-common/dh_installchangelogs.dch.trimmed debian/khmer-common/usr/share/doc/khmer-common/changelog.Debian install -p -m0644 ./CHANGELOG.md debian/khmer-common/usr/share/doc/khmer-common/changelog install -m0755 -d debian/liboxli1/usr/share/doc/liboxli1 install -p -m0644 debian/.debhelper/generated/liboxli1/dh_installchangelogs.dch.trimmed debian/liboxli1/usr/share/doc/liboxli1/changelog.Debian install -p -m0644 ./CHANGELOG.md debian/liboxli1/usr/share/doc/liboxli1/changelog dh_installman -O--buildsystem=pybuild install -m0755 -d debian/khmer/usr/share/man/man1/ install -p -m0644 ./debian/khmer.1 debian/khmer/usr/share/man/man1/khmer.1 man-recode --to-code UTF-8 --suffix .dh-new debian/khmer/usr/share/man/man1/khmer.1 mv debian/khmer/usr/share/man/man1/khmer.1.dh-new debian/khmer/usr/share/man/man1/khmer.1 chmod 0644 -- debian/khmer/usr/share/man/man1/khmer.1 dh_python3 -O--buildsystem=pybuild D: dh_python3 dh_python3:179: version: 6.20240422 D: dh_python3 dh_python3:180: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:181: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=['--buildsystem=pybuild']) D: dh_python3 dh_python3:182: supported Python versions: 3.11,3.12 (default=3.11) D: dh_python3 debhelper:166: skipping package khmer-common (missing ${python3:Depends} in Depends/Recommends) D: dh_python3 debhelper:166: skipping package liboxli1 (missing ${python3:Depends} in Depends/Recommends) D: dh_python3 debhelper:166: skipping package liboxli-dev (missing ${python3:Depends} in Depends/Recommends) D: dh_python3 debhelper:174: source=khmer, binary packages=['khmer'] D: dh_python3 dh_python3:204: processing package khmer... D: dh_python3 fs:50: moving files from debian/khmer/usr/lib/python3.11/dist-packages to debian/khmer/usr/lib/python3/dist-packages/ D: dh_python3 fs:50: moving files from debian/khmer/usr/lib/python3.12/dist-packages to debian/khmer/usr/lib/python3/dist-packages/ D: dh_python3 tools:101: fix_shebang (debian/khmer/usr/bin/khmer): doesn't look like a shebang: #!/bin/sh D: dh_python3 fs:246: removing dist-packages/.pytest_cache D: dh_python3 fs:335: package khmer details = {'requires.txt': {'debian/khmer/usr/lib/python3/dist-packages/khmer-3.0.0a3.egg-info/requires.txt'}, 'egg-info': {'debian/khmer/usr/lib/python3/dist-packages/khmer-3.0.0a3.egg-info/PKG-INFO'}, 'dist-info': set(), 'nsp.txt': set(), 'shebangs': set(), 'public_vers': {Version('3')}, 'private_dirs': {'/usr/lib/khmer': {'shebangs': {/usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3}, 'compile': True}}, 'compile': True, 'ext_vers': {Version('3.12'), Version('3.11')}, 'ext_no_version': set()} D: dh_python3 depends:103: generating dependencies for package khmer D: dh_python3 pydist:173: trying to find dependency for screed>=1.0 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for argparse>=1.2.1 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:218: dependency: requirement already has hardcoded version D: dh_python3 depends:253: D={'python3-screed', 'python3 (>= 3.11~)', 'python3 (<< 3.13)', 'python3 (>= 3.2) | python3-supported-max (<< 2.6) | python3-supported-min (>= 2.7)', 'python3:any'}; R=[]; S=[]; E=[], B=[]; RT=[('/usr/lib/khmer', '')] dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild install -m0755 -d debian/khmer/usr/share/lintian/overrides install -p -m0644 debian/khmer.lintian-overrides debian/khmer/usr/share/lintian/overrides/khmer install -m0755 -d debian/liboxli1/usr/share/lintian/overrides install -p -m0644 debian/liboxli1.lintian-overrides debian/liboxli1/usr/share/lintian/overrides/liboxli1 dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt ln -s ../../CITATION debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.min.js ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/js/bootstrap.min.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.min.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.js ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/js/bootstrap.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-ExtraLight.otf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/OTF/SourceSerifPro-ExtraLight.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-ExtraLight.otf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Semibold.otf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/OTF/SourceSerifPro-Semibold.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Semibold.otf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Light.otf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/OTF/SourceSerifPro-Light.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Light.otf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Regular.otf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/OTF/SourceSerifPro-Regular.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Regular.otf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Bold.otf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/OTF/SourceSerifPro-Bold.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Bold.otf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Black.otf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/OTF/SourceSerifPro-Black.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Black.otf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Black.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/EOT/SourceSerifPro-Black.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Black.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Light.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/EOT/SourceSerifPro-Light.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Light.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Semibold.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/EOT/SourceSerifPro-Semibold.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Semibold.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Bold.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/EOT/SourceSerifPro-Bold.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Bold.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-ExtraLight.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/EOT/SourceSerifPro-ExtraLight.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-ExtraLight.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Regular.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/EOT/SourceSerifPro-Regular.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Regular.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Light.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/TTF/SourceSerifPro-Light.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Light.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Black.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/TTF/SourceSerifPro-Black.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Black.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Semibold.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/TTF/SourceSerifPro-Semibold.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Semibold.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-ExtraLight.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/TTF/SourceSerifPro-ExtraLight.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-ExtraLight.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Bold.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/TTF/SourceSerifPro-Bold.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Bold.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Regular.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/TTF/SourceSerifPro-Regular.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Regular.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Regular.otf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Regular.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Regular.otf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-ExtraLight.otf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-ExtraLight.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-ExtraLight.otf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Semibold.otf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Semibold.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Semibold.otf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Black.otf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Black.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Black.otf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Bold.otf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Bold.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Bold.otf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Light.otf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Light.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Light.otf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Semibold.ttf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Semibold.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Semibold.ttf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Black.ttf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Black.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Black.ttf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-ExtraLight.ttf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-ExtraLight.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-ExtraLight.ttf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Bold.ttf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Bold.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Bold.ttf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Regular.ttf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Regular.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Regular.ttf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Light.ttf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Light.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Light.ttf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/source-serif-pro.css ln -s ../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/source-serif-pro.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/source-serif-pro.css rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/SourceSerifProReadMe.html ln -s ../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/SourceSerifProReadMe.html debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/SourceSerifProReadMe.html rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/bower.json ln -s ../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/bower.json debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/bower.json rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/README.md ln -s 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../../../../javascript/sphinxdoc/1.0/language_data.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js ln -s ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/sphinx_highlight.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js ln -s ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js ln -s ../../../../javascript/sphinxdoc/1.0/doctools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js rm -f debian/liboxli-dev/usr/lib/x86_64-linux-gnu/liboxli.so ln -s liboxli.so.1 debian/liboxli-dev/usr/lib/x86_64-linux-gnu/liboxli.so dh_strip_nondeterminism -O--buildsystem=pybuild Using 1708169923 as canonical time Normalizing debian/khmer-common/usr/share/doc/khmer-common/html/_images/partitioning-workflow.png using File::StripNondeterminism::handlers::png Normalizing debian/khmer-common/usr/share/doc/khmer-common/html/_static/minus.png using File::StripNondeterminism::handlers::png Normalizing debian/khmer-common/usr/share/doc/khmer-common/html/_static/plus.png using File::StripNondeterminism::handlers::png Normalizing debian/khmer-common/usr/share/doc/khmer-common/html/_static/file.png using File::StripNondeterminism::handlers::png Normalizing debian/khmer-common/usr/share/doc/khmer-common/html/_images/artifact-removal.png using File::StripNondeterminism::handlers::png Using 1708169923 as canonical time Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/test-abund-read-2.fa.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.truncated.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fq.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/empty-file.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/goodversion-k12.ht.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fa.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/test-reads.fq.gz using File::StripNondeterminism::handlers::gzip dh_compress -O--buildsystem=pybuild cd debian/khmer-common cd debian/khmer cd debian/liboxli1 cd debian/liboxli-dev chmod a-x usr/share/doc/khmer-common/CITATION usr/share/doc/khmer-common/changelog usr/share/doc/khmer-common/changelog.Debian gzip -9nf usr/share/doc/khmer-common/CITATION usr/share/doc/khmer-common/changelog usr/share/doc/khmer-common/changelog.Debian chmod a-x usr/share/doc/liboxli1/changelog usr/share/doc/liboxli1/changelog.Debian chmod a-x usr/share/doc/khmer/changelog usr/share/doc/khmer/changelog.Debian usr/share/man/man1/khmer.1 chmod a-x usr/share/doc/liboxli-dev/changelog usr/share/doc/liboxli-dev/changelog.Debian gzip -9nf usr/share/doc/khmer/changelog usr/share/doc/khmer/changelog.Debian usr/share/man/man1/khmer.1 gzip -9nf usr/share/doc/liboxli1/changelog usr/share/doc/liboxli1/changelog.Debian cd '/build/reproducible-path/khmer-3.0.0~a3+dfsg' gzip -9nf usr/share/doc/liboxli-dev/changelog usr/share/doc/liboxli-dev/changelog.Debian cd '/build/reproducible-path/khmer-3.0.0~a3+dfsg' cd '/build/reproducible-path/khmer-3.0.0~a3+dfsg' rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt.gz ln -s ../../CITATION.gz debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt.gz cd '/build/reproducible-path/khmer-3.0.0~a3+dfsg' dh_fixperms -O--buildsystem=pybuild find debian/liboxli1 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/liboxli-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/khmer ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/khmer-common ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/liboxli1/usr/share/doc -type f -a -true -a ! -regex 'debian/liboxli1/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/liboxli-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/khmer/usr/share/doc -type f -a -true -a ! -regex 'debian/khmer/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/khmer-common/usr/share/doc -type f -a -true -a ! -regex 'debian/khmer-common/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli1/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/liboxli-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/khmer/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/khmer-common/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/liboxli-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli1/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/khmer/usr/share/man debian/khmer/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/khmer-common -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli1 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/khmer -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/liboxli1/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/khmer/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/khmer/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dwz -- debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 install -m0755 -d debian/khmer/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/khmer/usr/lib/debug/.dwz/x86_64-linux-gnu/khmer.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/khmer.debug -- debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashset.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashset.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hllcounter.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hllcounter.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/labeling.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/legacy_partitioning.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/readaligner.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/traversal.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-312-x86_64-linux-gnu.so objcopy --compress-debug-sections debian/khmer/usr/lib/debug/.dwz/x86_64-linux-gnu/khmer.debug chmod 0644 -- debian/khmer/usr/lib/debug/.dwz/x86_64-linux-gnu/khmer.debug dh_strip -a -O--buildsystem=pybuild strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives -R .gnu.lto_\* -R .gnu.debuglto_\* -N __gnu_lto_slim -N __gnu_lto_v1 debian/liboxli-dev/usr/lib/x86_64-linux-gnu/liboxli.a install -m0755 -d debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/f9 objcopy --only-keep-debug --compress-debug-sections debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/f9/83865f2dca220ede538fd3cc71811e155e54d5.debug install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/e9 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-312-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/e9/14bb37f7bfe4d5bbbf9e65bd3bfe0c8c66cd1c.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/e9/14bb37f7bfe4d5bbbf9e65bd3bfe0c8c66cd1c.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-312-x86_64-linux-gnu.so chmod 0644 -- debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/f9/83865f2dca220ede538fd3cc71811e155e54d5.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/e9/14bb37f7bfe4d5bbbf9e65bd3bfe0c8c66cd1c.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/f9/83865f2dca220ede538fd3cc71811e155e54d5.debug debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/fe objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-311-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/fe/27b0b6080153e9991fd6125fad380b8639115d.debug install -m0755 -d debian/.debhelper/liboxli1/dbgsym-root/usr/share/doc ln -s liboxli1 debian/.debhelper/liboxli1/dbgsym-root/usr/share/doc/liboxli1-dbgsym install -m0755 -d debian/.debhelper/liboxli1 chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/fe/27b0b6080153e9991fd6125fad380b8639115d.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/fe/27b0b6080153e9991fd6125fad380b8639115d.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/82 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/82/bd707aa27744b01581519b1b5bf7267b16e6b9.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/82/bd707aa27744b01581519b1b5bf7267b16e6b9.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/82/bd707aa27744b01581519b1b5bf7267b16e6b9.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/0c objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-312-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/0c/2f5ebcdbb32ec2b0de5cf3ecf487fd6b822c58.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/0c/2f5ebcdbb32ec2b0de5cf3ecf487fd6b822c58.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/0c/2f5ebcdbb32ec2b0de5cf3ecf487fd6b822c58.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-312-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/da objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hllcounter.cpython-312-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/da/3473b258c2bc88c3afa6f7c7b77e15610d7b7b.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/da/3473b258c2bc88c3afa6f7c7b77e15610d7b7b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hllcounter.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/da/3473b258c2bc88c3afa6f7c7b77e15610d7b7b.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hllcounter.cpython-312-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/b9 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-312-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/b9/0b939b0723c2813eafa28cbaf5d0ff7dcd6635.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/b9/0b939b0723c2813eafa28cbaf5d0ff7dcd6635.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/b9/0b939b0723c2813eafa28cbaf5d0ff7dcd6635.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-312-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/a4 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/a4/91cc82750000b09814dc2b7842913e33e8ced9.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/a4/91cc82750000b09814dc2b7842913e33e8ced9.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/a4/91cc82750000b09814dc2b7842913e33e8ced9.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/09 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-312-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/09/0e2b3adea43e719a886c1f1dc8634448fdef87.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/09/0e2b3adea43e719a886c1f1dc8634448fdef87.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/09/0e2b3adea43e719a886c1f1dc8634448fdef87.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-312-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/c6 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/c6/8f27ae495401f0fc7f89096d89518ffe542d5a.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/c6/8f27ae495401f0fc7f89096d89518ffe542d5a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/c6/8f27ae495401f0fc7f89096d89518ffe542d5a.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/95 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/95/05740201b614d00856c853350c2a720c2717b3.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/95/05740201b614d00856c853350c2a720c2717b3.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/95/05740201b614d00856c853350c2a720c2717b3.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/f1 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-312-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/f1/193eb1e6a0089cf76f42af0c398dfe3fed22e5.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/f1/193eb1e6a0089cf76f42af0c398dfe3fed22e5.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/f1/193eb1e6a0089cf76f42af0c398dfe3fed22e5.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-312-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/40 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashset.cpython-311-x86_64-linux-gnu.so 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debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/db/62b9e41cb87550d67716b557c040d4402958fa.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/db/62b9e41cb87550d67716b557c040d4402958fa.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/fc objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/fc/b94e4e92975352c309f5af870322db338f2341.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/fc/b94e4e92975352c309f5af870322db338f2341.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/fc/b94e4e92975352c309f5af870322db338f2341.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/1d objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/1d/bc3610e38c1344ba3b0c94f1adf7f5cb43f1be.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/1d/bc3610e38c1344ba3b0c94f1adf7f5cb43f1be.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/1d/bc3610e38c1344ba3b0c94f1adf7f5cb43f1be.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/d3 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/d3/102f82c81bae06823b18bf55868fff3d0be7b7.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/d3/102f82c81bae06823b18bf55868fff3d0be7b7.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/d3/102f82c81bae06823b18bf55868fff3d0be7b7.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/bf objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/labeling.cpython-312-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/bf/c8e0cd7153df946d6f9ce1d1caa9773f980299.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/bf/c8e0cd7153df946d6f9ce1d1caa9773f980299.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/labeling.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/bf/c8e0cd7153df946d6f9ce1d1caa9773f980299.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/labeling.cpython-312-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/2e objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/traversal.cpython-312-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/2e/61645fc5dc5ddbebddcb4e1d831ee00df4abe4.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/2e/61645fc5dc5ddbebddcb4e1d831ee00df4abe4.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/traversal.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/2e/61645fc5dc5ddbebddcb4e1d831ee00df4abe4.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/traversal.cpython-312-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/71 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-312-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/71/ff63217f0a6fe054578cbc09341501b683210d.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/71/ff63217f0a6fe054578cbc09341501b683210d.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/71/ff63217f0a6fe054578cbc09341501b683210d.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-312-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/03 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashset.cpython-312-x86_64-linux-gnu.so 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--remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/readaligner.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/c5/7d61367b31c4f5e03452b04dcc779a08a0f64c.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/readaligner.cpython-312-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/10 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/legacy_partitioning.cpython-312-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/10/0fbedadf1a4f173fe981e627e988db24d7bbb9.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/10/0fbedadf1a4f173fe981e627e988db24d7bbb9.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded 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--add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/61/409c4f9fb0420590080316e9c022090d6550b6.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/khmer/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/khmer/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/khmer/usr/lib/debug install -m0755 -d debian/.debhelper/khmer/dbgsym-root/usr/share/doc ln -s khmer debian/.debhelper/khmer/dbgsym-root/usr/share/doc/khmer-dbgsym install -m0755 -d debian/.debhelper/khmer dh_makeshlibs -a -O--buildsystem=pybuild rm -f debian/khmer/DEBIAN/shlibs rm -f debian/liboxli1/DEBIAN/shlibs install -m0755 -d debian/liboxli1/DEBIAN echo "liboxli 1 liboxli1 (>= 3.0.0~a3+dfsg)" >> debian/liboxli1/DEBIAN/shlibs chmod 0644 -- debian/liboxli1/DEBIAN/shlibs mv debian/.debhelper/generated/liboxli1/triggers.new debian/.debhelper/generated/liboxli1/triggers rm -f debian/liboxli-dev/DEBIAN/shlibs dh_shlibdeps -a -O--buildsystem=pybuild install -m0755 -d debian/liboxli1/DEBIAN dpkg-shlibdeps -Tdebian/liboxli1.substvars debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 install -m0755 -d debian/khmer/DEBIAN dpkg-shlibdeps -Tdebian/khmer.substvars debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hllcounter.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/legacy_partitioning.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashset.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/traversal.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/labeling.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/readaligner.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/labeling.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/traversal.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashset.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hllcounter.cpython-311-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/readaligner.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/legacy_partitioning.cpython-312-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-311-x86_64-linux-gnu.so dpkg-shlibdeps: warning: symbol inflateEnd used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol inflate used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzerror used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzopen used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzdirect used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol inflateInit2_ used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzclose used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gztell64 used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol BZ2_bzRead used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzclearerr used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: 13 other similar warnings have been skipped (use -v to see them all) dh_installdeb -O--buildsystem=pybuild install -m0755 -d debian/khmer-common/DEBIAN cp -f debian/khmer-common.postinst debian/khmer-common/DEBIAN/postinst [META] Replace #TOKEN#s in "debian/khmer-common/DEBIAN/postinst" chmod 0755 -- debian/khmer-common/DEBIAN/postinst cp -f debian/khmer-common.postrm debian/khmer-common/DEBIAN/postrm [META] Replace #TOKEN#s in "debian/khmer-common/DEBIAN/postrm" chmod 0755 -- debian/khmer-common/DEBIAN/postrm install -m0755 -d debian/khmer/DEBIAN printf '#!/bin/sh\nset -e\n' > debian/khmer/DEBIAN/postinst cat debian/khmer.postinst.debhelper >> debian/khmer/DEBIAN/postinst chmod 0755 -- debian/khmer/DEBIAN/postinst printf '#!/bin/sh\nset -e\n' > debian/khmer/DEBIAN/prerm cat debian/khmer.prerm.debhelper >> debian/khmer/DEBIAN/prerm chmod 0755 -- debian/khmer/DEBIAN/prerm install -m0755 -d debian/liboxli1/DEBIAN install -p -m0644 debian/.debhelper/generated/liboxli1/triggers debian/liboxli1/DEBIAN/triggers install -m0755 -d debian/liboxli-dev/DEBIAN dh_gencontrol -O--buildsystem=pybuild install -m0755 -d debian/liboxli-dev/DEBIAN echo misc:Depends= >> debian/liboxli-dev.substvars echo misc:Pre-Depends= >> debian/liboxli-dev.substvars dpkg-gencontrol -pliboxli-dev -ldebian/changelog -Tdebian/liboxli-dev.substvars -cdebian/control -Pdebian/liboxli-dev install -m0755 -d debian/khmer-common/DEBIAN echo misc:Depends= >> debian/khmer-common.substvars echo misc:Pre-Depends= >> debian/khmer-common.substvars dpkg-gencontrol -pkhmer-common -ldebian/changelog -Tdebian/khmer-common.substvars -cdebian/control -Pdebian/khmer-common install -m0755 -d debian/liboxli1/DEBIAN echo misc:Depends= >> debian/liboxli1.substvars echo misc:Pre-Depends= >> debian/liboxli1.substvars install -m0755 -d debian/.debhelper/liboxli1/dbgsym-root/DEBIAN dpkg-gencontrol -pliboxli1 -ldebian/changelog -Tdebian/liboxli1.substvars -cdebian/control -Pdebian/.debhelper/liboxli1/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=liboxli1-dbgsym "-DDepends=liboxli1 (= \${binary:Version})" "-DDescription=debug symbols for liboxli1" -DBuild-Ids=f983865f2dca220ede538fd3cc71811e155e54d5 -DSection=debug -UReplaces -UBreaks install -m0755 -d debian/khmer/DEBIAN echo misc:Depends= >> debian/khmer.substvars echo misc:Pre-Depends= >> debian/khmer.substvars install -m0755 -d debian/.debhelper/khmer/dbgsym-root/DEBIAN dpkg-gencontrol -pkhmer -ldebian/changelog -Tdebian/khmer.substvars -cdebian/control -Pdebian/.debhelper/khmer/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=khmer-dbgsym "-DDepends=khmer (= \${binary:Version})" "-DDescription=debug symbols for khmer" "-DBuild-Ids=030ecdf6c336dbffdbecb3fc48c9307ec1fb3f05 090e2b3adea43e719a886c1f1dc8634448fdef87 0c2f5ebcdbb32ec2b0de5cf3ecf487fd6b822c58 100fbedadf1a4f173fe981e627e988db24d7bbb9 1dbc3610e38c1344ba3b0c94f1adf7f5cb43f1be 2e61645fc5dc5ddbebddcb4e1d831ee00df4abe4 403fce65e9760053360a62ffc6b8c3289fbf9e52 61409c4f9fb0420590080316e9c022090d6550b6 71ff63217f0a6fe054578cbc09341501b683210d 82bd707aa27744b01581519b1b5bf7267b16e6b9 9505740201b614d00856c853350c2a720c2717b3 9f29b2dc57c5e42d3562199ba8029cf2d6219dc4 a491cc82750000b09814dc2b7842913e33e8ced9 b90b939b0723c2813eafa28cbaf5d0ff7dcd6635 bfc8e0cd7153df946d6f9ce1d1caa9773f980299 c57d61367b31c4f5e03452b04dcc779a08a0f64c c68f27ae495401f0fc7f89096d89518ffe542d5a d3102f82c81bae06823b18bf55868fff3d0be7b7 da3473b258c2bc88c3afa6f7c7b77e15610d7b7b db62b9e41cb87550d67716b557c040d4402958fa e914bb37f7bfe4d5bbbf9e65bd3bfe0c8c66cd1c f1193eb1e6a0089cf76f42af0c398dfe3fed22e5 fcb94e4e92975352c309f5af870322db338f2341 fe27b0b6080153e9991fd6125fad380b8639115d" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/liboxli-dev/DEBIAN/control chmod 0644 -- debian/khmer-common/DEBIAN/control chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/DEBIAN/control dpkg-gencontrol -pkhmer -ldebian/changelog -Tdebian/khmer.substvars -cdebian/control -Pdebian/khmer chmod 0644 -- debian/.debhelper/liboxli1/dbgsym-root/DEBIAN/control dpkg-gencontrol -pliboxli1 -ldebian/changelog -Tdebian/liboxli1.substvars -cdebian/control -Pdebian/liboxli1 chmod 0644 -- debian/liboxli1/DEBIAN/control chmod 0644 -- debian/khmer/DEBIAN/control dh_md5sums -O--buildsystem=pybuild install -m0755 -d debian/khmer/DEBIAN install -m0755 -d debian/khmer-common/DEBIAN install -m0755 -d debian/liboxli-dev/DEBIAN cd debian/khmer >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/liboxli-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/khmer-common >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums install -m0755 -d debian/liboxli1/DEBIAN cd debian/liboxli1 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/liboxli-dev/DEBIAN/md5sums chmod 0644 -- debian/khmer-common/DEBIAN/md5sums chmod 0644 -- debian/liboxli1/DEBIAN/md5sums install -m0755 -d debian/.debhelper/liboxli1/dbgsym-root/DEBIAN cd debian/.debhelper/liboxli1/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/liboxli1/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/khmer/DEBIAN/md5sums install -m0755 -d debian/.debhelper/khmer/dbgsym-root/DEBIAN cd debian/.debhelper/khmer/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/DEBIAN/md5sums dh_builddeb -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/khmer-common .. dpkg-deb --root-owner-group --build debian/khmer .. dpkg-deb --root-owner-group --build debian/.debhelper/khmer/dbgsym-root .. dpkg-deb --root-owner-group --build debian/liboxli1 .. dpkg-deb --root-owner-group --build debian/liboxli-dev .. dpkg-deb --root-owner-group --build debian/.debhelper/liboxli1/dbgsym-root .. dpkg-deb: building package 'liboxli1' in '../liboxli1_3.0.0~a3+dfsg-8_amd64.deb'. dpkg-deb: building package 'liboxli1-dbgsym' in '../liboxli1-dbgsym_3.0.0~a3+dfsg-8_amd64.deb'. dpkg-deb: building package 'khmer' in '../khmer_3.0.0~a3+dfsg-8_amd64.deb'. dpkg-deb: building package 'khmer-dbgsym' in '../khmer-dbgsym_3.0.0~a3+dfsg-8_amd64.deb'. dpkg-deb: building package 'liboxli-dev' in '../liboxli-dev_3.0.0~a3+dfsg-8_amd64.deb'. dpkg-deb: building package 'khmer-common' in '../khmer-common_3.0.0~a3+dfsg-8_all.deb'. dpkg-genbuildinfo --build=binary -O../khmer_3.0.0~a3+dfsg-8_amd64.buildinfo dpkg-genchanges --build=binary -O../khmer_3.0.0~a3+dfsg-8_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/816689/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/816689/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/816689 and its subdirectories I: Current time: Sun May 12 03:29:10 +14 2024 I: pbuilder-time-stamp: 1715434150