I: pbuilder: network access will be disabled during build I: Current time: Mon Oct 21 10:08:42 +14 2024 I: pbuilder-time-stamp: 1729454922 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 [flye_2.9.5+dfsg-1.dsc] I: copying [./flye_2.9.5+dfsg.orig.tar.xz] I: copying [./flye_2.9.5+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Aug 31 11:11:18 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./flye_2.9.5+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting flye in flye-2.9.5+dfsg dpkg-source: info: unpacking flye_2.9.5+dfsg.orig.tar.xz dpkg-source: info: unpacking flye_2.9.5+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs.patch dpkg-source: info: applying cppflags.patch dpkg-source: info: applying python3.12.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/426167/tmp/hooks/D01_modify_environment starting debug: Running on infom01-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 Oct 20 20:08 /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/426167/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/426167/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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(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=12 ' 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=cd82346ffb5d41009ba67691b6dda356 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=426167 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.iOhKqZu1/pbuilderrc_g2DV --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.iOhKqZu1/b2 --logfile b2/build.log flye_2.9.5+dfsg-1.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' I: uname -a Linux i-capture-the-hostname 6.1.0-26-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/426167/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, python3, python3-setuptools, liblemon-dev, libminimap2-dev, samtools, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19799 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 python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on liblemon-dev; however: Package liblemon-dev is not installed. pbuilder-satisfydepends-dummy depends on libminimap2-dev; however: Package libminimap2-dev is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev 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: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libamd3{a} libarchive-zip-perl{a} libbrotli1{a} libcolamd3{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglpk40{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblemon-dev{a} liblemon1.3.1{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libminimap2-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libsuitesparseconfig7{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-autocommand{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 88 newly installed, 0 to remove and 0 not upgraded. Need to get 33.4 MB of archives. After unpacking 124 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.6-1 [814 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.3-1 [105 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 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 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-9 [97.2 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 44 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 58 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 74.1.2-2 [736 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20240824 [109 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libsuitesparseconfig7 amd64 1:7.8.2+dfsg-2 [23.3 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libamd3 amd64 1:7.8.2+dfsg-2 [40.2 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libcolamd3 amd64 1:7.8.2+dfsg-2 [32.0 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3 [187 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.4.0-1 [63.1 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.10.1-2 [360 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libltdl7 amd64 2.4.7-7+b1 [393 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libglpk40 amd64 5.0-1+b1 [397 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 liblemon1.3.1 amd64 1.3.1+dfsg-6+b1 [55.3 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 liblemon-dev amd64 1.3.1+dfsg-6+b1 [325 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libminimap2-dev amd64 2.27+dfsg-1+b1 [130 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.20-3 [653 kB] Fetched 33.4 MB in 3s (11.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19799 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.6-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_amd64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:amd64 (3.12.6-1) ... Setting up libexpat1:amd64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20119 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_amd64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21191 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sensible-utils. 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Setting up m4 (1.4.19-4) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Oct 20 20:09:15 UTC 2024. Universal Time is now: Sun Oct 20 20:09:15 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libltdl7:amd64 (2.4.7-7+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.4.0-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libsuitesparseconfig7:amd64 (1:7.8.2+dfsg-2) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:amd64 (1.6.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.0-7) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... 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 (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libamd3:amd64 (1:7.8.2+dfsg-2) ... Setting up libtool (2.4.7-7) ... Setting up libcolamd3:amd64 (1:7.8.2+dfsg-2) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... 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Setting up python3-autocommand (2.2.2-3) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-setuptools (74.1.2-2) ... Setting up dh-python (6.20240824) ... Processing triggers for libc-bin (2.40-3) ... 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/426167/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/426167/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/flye-2.9.5+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 > ../flye_2.9.5+dfsg-1_source.changes dpkg-buildpackage: info: source package flye dpkg-buildpackage: info: source version 2.9.5+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/flye-2.9.5+dfsg' dh_auto_clean I: pybuild base:311: python3.12 setup.py clean running clean removing '/build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/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 find src -name "*.o" -delete rm -f bin/flye-modules rm -rf flye.egg-info/ make[1]: Leaving directory '/build/reproducible-path/flye-2.9.5+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye copying flye/__build__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye copying flye/main.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye copying flye/__version__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye copying flye/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/assembly copying flye/assembly/assemble.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/assembly copying flye/assembly/repeat_graph.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/assembly copying flye/assembly/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/assembly copying flye/assembly/scaffolder.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/assembly creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config copying flye/config/configurator.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config copying flye/config/py_cfg.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config copying flye/config/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing copying flye/polishing/bubbles.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing copying flye/polishing/consensus.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing copying flye/polishing/alignment.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing copying flye/polishing/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing copying flye/polishing/polish.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils copying flye/utils/fasta_parser.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils copying flye/utils/bytes2human.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils copying flye/utils/sam_parser.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils copying flye/utils/utils.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils copying flye/utils/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/repeat_graph copying flye/repeat_graph/repeat_graph.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/repeat_graph copying flye/repeat_graph/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/repeat_graph copying flye/repeat_graph/graph_alignment.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/repeat_graph creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids copying flye/short_plasmids/plasmids.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids copying flye/short_plasmids/circular_sequences.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids copying flye/short_plasmids/unmapped_reads.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids copying flye/short_plasmids/utils.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids copying flye/short_plasmids/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle copying flye/trestle/trestle_config.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle copying flye/trestle/trestle.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle copying flye/trestle/graph_resolver.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle copying flye/trestle/divergence.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle copying flye/trestle/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests copying flye/tests/test_toy.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests copying flye/tests/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/nano_r94_g36_substitutions.mat -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_corrected_reads.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_defaults.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_nano_hq.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/nano_r94_substitutions.mat -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/pacbio_chm13_substitutions.mat -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_raw_reads.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_hifi.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/pacbio_chm13_homopolymers.mat -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_subasm.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/pacbio_homopolymers.mat -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/nano_r94_homopolymers.mat -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/nano_r94_g36_homopolymers.mat -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/pacbio_substitutions.mat -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/data copying flye/tests/data/ecoli_500kb_reads.fastq.gz -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/data copying flye/tests/data/ecoli_500kb.fasta -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/data copying flye/tests/data/ecoli_500kb_reads_hifi.fastq.gz -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/data /build/reproducible-path/flye-2.9.5+dfsg/setup.py:35: DeprecationWarning: Use shutil.which instead of find_executable if not find_executable("make"): make[1]: Entering directory '/build/reproducible-path/flye-2.9.5+dfsg' make release -C src -j 4 make[2]: Entering directory '/build/reproducible-path/flye-2.9.5+dfsg/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG assemble/chimera.cpp -o assemble/chimera.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG assemble/extender.cpp -o assemble/extender.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG assemble/main_assemble.cpp -o assemble/main_assemble.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG assemble/parameters_estimator.cpp -o assemble/parameters_estimator.o assemble/main_assemble.cpp:214:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 214 | Logger::get().debug() << "Build date: " << __DATE__ << " " << __TIME__; | ^~~~~~~~ assemble/main_assemble.cpp:214:71: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 214 | Logger::get().debug() << "Build date: " << __DATE__ << " " << __TIME__; | ^~~~~~~~ In file included from assemble/../sequence/overlap.h:12, from assemble/chimera.h:7, from assemble/chimera.cpp:14: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ In file included from assemble/../sequence/overlap.h:12, from assemble/extender.h:10, from assemble/extender.cpp:14: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ In file included from assemble/../sequence/overlap.h:12, from assemble/main_assemble.cpp:14: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/alignment.cpp -o sequence/alignment.o In file included from sequence/overlap.h:12, from sequence/alignment.h:7, from sequence/alignment.cpp:8: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/consensus_generator.cpp -o sequence/consensus_generator.o In file included from sequence/../sequence/overlap.h:12, from sequence/consensus_generator.h:12, from sequence/consensus_generator.cpp:9: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/edlib.cpp -o sequence/edlib.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/overlap.cpp -o sequence/overlap.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/sequence.cpp -o sequence/sequence.o In file included from sequence/overlap.h:12, from sequence/overlap.cpp:19: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/sequence_container.cpp -o sequence/sequence_container.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/vertex_index.cpp -o sequence/vertex_index.o In file included from sequence/overlap.cpp:25: sequence/../common/bfcontainer.h: In instantiation of ‘BFContainer::BFIterator BFContainer::BFIterator::operator+(difference_type) const [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576; difference_type = long int]’: sequence/overlap.cpp:240:43: required from here 240 | matchesList.assign(vecMatches.begin() + extRangeBegin, | ^~~~~~~~~~~~~ sequence/../common/bfcontainer.h:182:30: warning: implicitly-declared ‘constexpr BFContainer<{anonymous}::KmerMatch>::BFIterator::BFIterator(const BFContainer<{anonymous}::KmerMatch>::BFIterator&)’ is deprecated [-Wdeprecated-copy] 182 | auto tmp = *this; | ^~~ sequence/../common/bfcontainer.h:141:21: note: because ‘BFContainer<{anonymous}::KmerMatch>::BFIterator’ has user-provided ‘BFContainer::BFIterator& BFContainer::BFIterator::operator=(const BFContainer::BFIterator&) [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576]’ 141 | BFIterator& operator=(const BFIterator &rhs) | ^~~~~~~~ sequence/../common/bfcontainer.h:183:39: warning: implicitly-declared ‘constexpr BFContainer<{anonymous}::KmerMatch>::BFIterator::BFIterator(const BFContainer<{anonymous}::KmerMatch>::BFIterator&)’ is deprecated [-Wdeprecated-copy] 183 | return tmp += n; | ^ sequence/../common/bfcontainer.h:141:21: note: because ‘BFContainer<{anonymous}::KmerMatch>::BFIterator’ has user-provided ‘BFContainer::BFIterator& BFContainer::BFIterator::operator=(const BFContainer::BFIterator&) [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576]’ 141 | BFIterator& operator=(const BFIterator &rhs) | ^~~~~~~~ sequence/../common/bfcontainer.h: In instantiation of ‘BFContainer::BFIterator BFContainer::BFIterator::operator-(difference_type) const [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576; difference_type = long int]’: /usr/include/c++/14/bits/stl_algo.h:1855:71: required from ‘_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = BFContainer<{anonymous}::KmerMatch>::BFIterator; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’ 1855 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, | ~~~~~~~^~~ /usr/include/c++/14/bits/stl_algo.h:1889:38: required from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = BFContainer<{anonymous}::KmerMatch>::BFIterator; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’ 1889 | std::__unguarded_partition_pivot(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1905:25: required from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = BFContainer<{anonymous}::KmerMatch>::BFIterator; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’ 1905 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1906 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1907 | __comp); | ~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:4804:18: required from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = BFContainer<{anonymous}::KmerMatch>::BFIterator; _Compare = OverlapDetector::getSeqOverlaps(const FastaRecord&, bool, OvlpDivStats&, int) const::]’ 4804 | std::__sort(__first, __last, __gnu_cxx::__ops::__iter_comp_iter(__comp)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence/overlap.cpp:204:11: required from here 204 | std::sort(vecMatches.begin(), vecMatches.end(), | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 | [](const KmerMatch& k1, const KmerMatch& k2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 206 | {return k1.extId != k2.extId ? k1.extId < k2.extId : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 207 | k1.curPos < k2.curPos;}); | ~~~~~~~~~~~~~~~~~~~~~~~~ sequence/../common/bfcontainer.h:193:30: warning: implicitly-declared ‘constexpr BFContainer<{anonymous}::KmerMatch>::BFIterator::BFIterator(const BFContainer<{anonymous}::KmerMatch>::BFIterator&)’ is deprecated [-Wdeprecated-copy] 193 | auto tmp = *this; | ^~~ sequence/../common/bfcontainer.h:141:21: note: because ‘BFContainer<{anonymous}::KmerMatch>::BFIterator’ has user-provided ‘BFContainer::BFIterator& BFContainer::BFIterator::operator=(const BFContainer::BFIterator&) [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576]’ 141 | BFIterator& operator=(const BFIterator &rhs) | ^~~~~~~~ sequence/../common/bfcontainer.h:194:39: warning: implicitly-declared ‘constexpr BFContainer<{anonymous}::KmerMatch>::BFIterator::BFIterator(const BFContainer<{anonymous}::KmerMatch>::BFIterator&)’ is deprecated [-Wdeprecated-copy] 194 | return tmp -= n; | ^ sequence/../common/bfcontainer.h:141:21: note: because ‘BFContainer<{anonymous}::KmerMatch>::BFIterator’ has user-provided ‘BFContainer::BFIterator& BFContainer::BFIterator::operator=(const BFContainer::BFIterator&) [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576]’ 141 | BFIterator& operator=(const BFIterator &rhs) | ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/graph_processing.cpp -o repeat_graph/graph_processing.o sequence/vertex_index.cpp: In member function ‘void KmerCounter::count(bool)’: sequence/vertex_index.cpp:380:28: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::atomic’ with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess] 380 | std::memset(_flatCounter, 0, COUNTER_LEN); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo/cuckoohash_map.hh:8, from sequence/vertex_index.h:15, from sequence/vertex_index.cpp:12: /usr/include/c++/14/atomic:758:12: note: ‘struct std::atomic’ declared here 758 | struct atomic : __atomic_base | ^~~~~~~~~~~~~~~~~~~~~ In file included from repeat_graph/../sequence/overlap.h:12, from repeat_graph/repeat_graph.h:11, from repeat_graph/graph_processing.h:10, from repeat_graph/graph_processing.cpp:7: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/haplotype_resolver.cpp -o repeat_graph/haplotype_resolver.o In file included from repeat_graph/../sequence/overlap.h:12, from repeat_graph/repeat_graph.h:11, from repeat_graph/haplotype_resolver.h:7, from repeat_graph/haplotype_resolver.cpp:1: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/main_repeat.cpp -o repeat_graph/main_repeat.o repeat_graph/main_repeat.cpp:152:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 152 | Logger::get().debug() << "Build date: " << __DATE__ << " " << __TIME__; | ^~~~~~~~ repeat_graph/main_repeat.cpp:152:71: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 152 | Logger::get().debug() << "Build date: " << __DATE__ << " " << __TIME__; | ^~~~~~~~ In file included from repeat_graph/../repeat_graph/../sequence/overlap.h:12, from repeat_graph/../repeat_graph/repeat_graph.h:11, from repeat_graph/main_repeat.cpp:17: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/multiplicity_inferer.cpp -o repeat_graph/multiplicity_inferer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/output_generator.cpp -o repeat_graph/output_generator.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/read_aligner.cpp -o repeat_graph/read_aligner.o In file included from repeat_graph/../sequence/overlap.h:12, from repeat_graph/repeat_graph.h:11, from repeat_graph/output_generator.h:13, from repeat_graph/output_generator.cpp:5: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ In file included from repeat_graph/../sequence/overlap.h:12, from repeat_graph/repeat_graph.h:11, from repeat_graph/multiplicity_inferer.h:7, from repeat_graph/multiplicity_inferer.cpp:5: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ In file included from repeat_graph/../sequence/overlap.h:12, from repeat_graph/repeat_graph.h:11, from repeat_graph/read_aligner.h:11, from repeat_graph/read_aligner.cpp:5: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/repeat_graph.cpp -o repeat_graph/repeat_graph.o In file included from repeat_graph/../sequence/overlap.h:12, from repeat_graph/repeat_graph.cpp:9: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/repeat_resolver.cpp -o repeat_graph/repeat_resolver.o In file included from repeat_graph/../sequence/overlap.h:12, from repeat_graph/repeat_graph.h:11, from repeat_graph/repeat_resolver.h:11, from repeat_graph/repeat_resolver.cpp:8: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG contigger/contig_extender.cpp -o contigger/contig_extender.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG contigger/main_contigger.cpp -o contigger/main_contigger.o contigger/main_contigger.cpp:159:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 159 | Logger::get().debug() << "Build date: " << __DATE__ << " " << __TIME__; | ^~~~~~~~ contigger/main_contigger.cpp:159:71: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 159 | Logger::get().debug() << "Build date: " << __DATE__ << " " << __TIME__; | ^~~~~~~~ In file included from contigger/../repeat_graph/../sequence/overlap.h:12, from contigger/../repeat_graph/repeat_graph.h:11, from contigger/contig_extender.h:7, from contigger/contig_extender.cpp:5: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ In file included from contigger/../repeat_graph/../sequence/overlap.h:12, from contigger/../repeat_graph/repeat_graph.h:11, from contigger/main_contigger.cpp:18: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -c -o polishing/alignment.o polishing/alignment.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -c -o polishing/bubble_processor.o polishing/bubble_processor.cpp In file included from polishing/bubble_processor.cpp:9: polishing/bubble_processor.h: In constructor ‘BubbleProcessor::BubbleProcessor(const std::string&, const std::string&, bool, bool)’: polishing/bubble_processor.h:48:35: warning: ‘BubbleProcessor::_dinucFixer’ will be initialized after [-Wreorder] 48 | const DinucleotideFixer _dinucFixer; | ^~~~~~~~~~~ polishing/bubble_processor.h:40:51: warning: ‘bool BubbleProcessor::_verbose’ [-Wreorder] 40 | bool _verbose; | ^~~~~~~~ polishing/bubble_processor.cpp:21:1: warning: when initialized here [-Wreorder] 21 | BubbleProcessor::BubbleProcessor(const std::string& subsMatPath, | ^~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -c -o polishing/dinucleotide_fixer.o polishing/dinucleotide_fixer.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -c -o polishing/general_polisher.o polishing/general_polisher.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -c -o polishing/homo_polisher.o polishing/homo_polisher.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -c -o polishing/main_polisher.o polishing/main_polisher.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -c -o polishing/subs_matrix.o polishing/subs_matrix.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG main.cpp -o main.o g++ assemble/chimera.o assemble/extender.o assemble/main_assemble.o assemble/parameters_estimator.o sequence/alignment.o sequence/consensus_generator.o sequence/edlib.o sequence/overlap.o sequence/sequence.o sequence/sequence_container.o sequence/vertex_index.o repeat_graph/graph_processing.o repeat_graph/haplotype_resolver.o repeat_graph/main_repeat.o repeat_graph/multiplicity_inferer.o repeat_graph/output_generator.o repeat_graph/read_aligner.o repeat_graph/repeat_graph.o repeat_graph/repeat_resolver.o contigger/contig_extender.o contigger/main_contigger.o polishing/alignment.o polishing/bubble_processor.o polishing/dinucleotide_fixer.o polishing/general_polisher.o polishing/homo_polisher.o polishing/main_polisher.o polishing/subs_matrix.o main.o -o /build/reproducible-path/flye-2.9.5+dfsg/bin/flye-modules -Wl,-z,relro -Wl,-z,now -lz -lminimap2 -pthread -std=c++11 -rdynamic make[2]: Leaving directory '/build/reproducible-path/flye-2.9.5+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/flye-2.9.5+dfsg' dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build; python3.12 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/flye/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/flye-2.9.5+dfsg/debian/flye 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 /build/reproducible-path/flye-2.9.5+dfsg/setup.py:35: DeprecationWarning: Use shutil.which instead of find_executable if not find_executable("make"): make[1]: Entering directory '/build/reproducible-path/flye-2.9.5+dfsg' make release -C src -j 4 make[2]: Entering directory '/build/reproducible-path/flye-2.9.5+dfsg/src' g++ assemble/chimera.o assemble/extender.o assemble/main_assemble.o assemble/parameters_estimator.o sequence/alignment.o sequence/consensus_generator.o sequence/edlib.o sequence/overlap.o sequence/sequence.o sequence/sequence_container.o sequence/vertex_index.o repeat_graph/graph_processing.o repeat_graph/haplotype_resolver.o repeat_graph/main_repeat.o repeat_graph/multiplicity_inferer.o repeat_graph/output_generator.o repeat_graph/read_aligner.o repeat_graph/repeat_graph.o repeat_graph/repeat_resolver.o contigger/contig_extender.o contigger/main_contigger.o polishing/alignment.o polishing/bubble_processor.o polishing/dinucleotide_fixer.o polishing/general_polisher.o polishing/homo_polisher.o polishing/main_polisher.o polishing/subs_matrix.o main.o -o /build/reproducible-path/flye-2.9.5+dfsg/bin/flye-modules -Wl,-z,relro -Wl,-z,now -lz -lminimap2 -pthread -std=c++11 -rdynamic make[2]: Leaving directory '/build/reproducible-path/flye-2.9.5+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/flye-2.9.5+dfsg' running install_lib creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12 creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle/trestle_config.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle/trestle.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle/graph_resolver.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle/divergence.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle/__pycache__ creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/assembly/assemble.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/assembly/repeat_graph.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/assembly/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/assembly/scaffolder.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/assembly/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly/__pycache__ creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing/bubbles.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing/consensus.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing/alignment.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing/polish.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing/__pycache__ creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils/fasta_parser.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils/bytes2human.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils/sam_parser.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils/utils.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/__build__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/repeat_graph copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/repeat_graph/repeat_graph.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/repeat_graph copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/repeat_graph/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/repeat_graph creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/repeat_graph/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/repeat_graph/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/repeat_graph/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/repeat_graph/graph_alignment.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/repeat_graph copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/main.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/configurator.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/py_cfg.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/nano_r94_g36_substitutions.mat -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/asm_corrected_reads.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/asm_defaults.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/asm_nano_hq.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/nano_r94_substitutions.mat -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/pacbio_chm13_substitutions.mat -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/asm_raw_reads.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/asm_hifi.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/pacbio_chm13_homopolymers.mat -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/asm_subasm.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/pacbio_homopolymers.mat -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/nano_r94_homopolymers.mat -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/nano_r94_g36_homopolymers.mat -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/pacbio_substitutions.mat -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/__version__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests/data copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/data/ecoli_500kb_reads.fastq.gz -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests/data copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/data/ecoli_500kb.fasta -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests/data copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/data/ecoli_500kb_reads_hifi.fastq.gz -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests/data copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/test_toy.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/__pycache__/test_toy.cpython-312.pyc -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids/plasmids.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids/circular_sequences.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids/unmapped_reads.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids/utils.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids/__pycache__ creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/__pycache__ byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle/trestle_config.py to trestle_config.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle/trestle.py to trestle.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle/graph_resolver.py to graph_resolver.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle/divergence.py to divergence.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly/assemble.py to assemble.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly/repeat_graph.py to repeat_graph.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly/scaffolder.py to scaffolder.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing/bubbles.py to bubbles.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing/consensus.py to consensus.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing/alignment.py to alignment.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing/polish.py to polish.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils/fasta_parser.py to fasta_parser.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils/bytes2human.py to bytes2human.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils/sam_parser.py to sam_parser.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils/utils.py to utils.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/__build__.py to __build__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/repeat_graph/repeat_graph.py to repeat_graph.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/repeat_graph/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/repeat_graph/graph_alignment.py to graph_alignment.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/main.py to main.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/configurator.py to configurator.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/py_cfg.py to py_cfg.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/__version__.py to __version__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests/test_toy.py to test_toy.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids/plasmids.py to plasmids.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids/circular_sequences.py to circular_sequences.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids/unmapped_reads.py to unmapped_reads.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids/utils.py to utils.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids/__init__.py to __init__.cpython-312.pyc running install_egg_info running egg_info creating flye.egg-info writing flye.egg-info/PKG-INFO writing dependency_links to flye.egg-info/dependency_links.txt writing entry points to flye.egg-info/entry_points.txt writing top-level names to flye.egg-info/top_level.txt writing manifest file 'flye.egg-info/SOURCES.txt' reading manifest file 'flye.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'flye.egg-info/SOURCES.txt' Copying flye.egg-info to /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye-2.9.5.egg-info Skipping SOURCES.txt running install_scripts Installing flye script to /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/bin Installing C++ binaries dh_install -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/flye-2.9.5+dfsg' dh_installchangelogs docs/NEWS.md make[1]: Leaving directory '/build/reproducible-path/flye-2.9.5+dfsg' dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild I: dh_python3 tools:113: replacing shebang in debian/flye/usr/bin/flye dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'flye' in '../flye_2.9.5+dfsg-1_amd64.deb'. dpkg-deb: building package 'flye-dbgsym' in '../flye-dbgsym_2.9.5+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../flye_2.9.5+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../flye_2.9.5+dfsg-1_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: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/426167/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/426167/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/426167 and its subdirectories I: Current time: Mon Oct 21 10:10:24 +14 2024 I: pbuilder-time-stamp: 1729455024