I: pbuilder: network access will be disabled during build I: Current time: Sun Apr 30 17:51:52 -12 2023 I: pbuilder-time-stamp: 1682920312 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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_2.9.1+dfsg-1.dsc] I: copying [./flye_2.9.1+dfsg.orig.tar.xz] I: copying [./flye_2.9.1+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Aug 23 02:47:47 2022 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./flye_2.9.1+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting flye in flye-2.9.1+dfsg dpkg-source: info: unpacking flye_2.9.1+dfsg.orig.tar.xz dpkg-source: info: unpacking flye_2.9.1+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1557405/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='456ca0a037af4ddbbb2e6f9ad1d5fc6a' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1557405' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Rsc8kJgp/pbuilderrc_tkt8 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Rsc8kJgp/b1 --logfile b1/build.log flye_2.9.1+dfsg-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos1-amd64 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 09:23 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:23 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 04:31 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar -rwxr-xr-x 1 root root 14520 Nov 2 04:31 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/1557405/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, 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 ... 19596 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on 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} libamd2{a} libarchive-zip-perl{a} libbrotli1{a} libcolamd2{a} libcurl3-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglpk40{a} libhts3{a} libhtscodecs2{a} libicu72{a} libldap-2.5-0{a} liblemon-dev{a} liblemon1.3.1{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libminimap2-dev{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libsuitesparseconfig5{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} readline-common{a} samtools{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 69 newly installed, 0 to remove and 0 not upgraded. Need to get 30.4 MB of archives. After unpacking 113 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-2 [131 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libsuitesparseconfig5 amd64 1:5.12.0+dfsg-2 [23.9 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libamd2 amd64 1:5.12.0+dfsg-2 [36.2 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libcolamd2 amd64 1:5.12.0+dfsg-2 [32.9 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-9 [381 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libltdl7 amd64 2.4.7-5 [393 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libglpk40 amd64 5.0-1 [400 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 liblemon1.3.1 amd64 1.3.1+dfsg-6 [53.2 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 liblemon-dev amd64 1.3.1+dfsg-6 [323 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libminimap2-dev amd64 2.24+dfsg-3+b1 [128 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-2 [103 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 samtools amd64 1.16.1-1 [607 kB] Fetched 30.4 MB in 1s (28.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... 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 ... 19912 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... 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 ... 20346 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/flye-2.9.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../flye_2.9.1+dfsg-1_source.changes dpkg-buildpackage: info: source package flye dpkg-buildpackage: info: source version 2.9.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/flye-2.9.1+dfsg' dh_auto_clean I: pybuild base:240: python3.11 setup.py clean running clean removing '/build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it find src -name "*.o" -delete rm -f bin/flye-modules rm -rf flye.egg-info/ make[1]: Leaving directory '/build/flye-2.9.1+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py build running build running build_py creating /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye copying flye/six.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye copying flye/main.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye copying flye/__version__.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye copying flye/__init__.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye copying flye/__build__.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye creating /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/assembly copying flye/assembly/scaffolder.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/assembly copying flye/assembly/repeat_graph.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/assembly copying flye/assembly/assemble.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/assembly copying flye/assembly/__init__.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/assembly creating /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config copying flye/config/py_cfg.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config copying flye/config/configurator.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config copying flye/config/__init__.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config creating /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/polishing copying flye/polishing/alignment.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/polishing copying flye/polishing/polish.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/polishing copying flye/polishing/consensus.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/polishing copying flye/polishing/bubbles.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/polishing copying flye/polishing/__init__.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/polishing creating /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/utils copying flye/utils/utils.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/utils copying flye/utils/sam_parser.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/utils copying flye/utils/fasta_parser.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/utils copying flye/utils/bytes2human.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/utils copying flye/utils/__init__.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/utils creating /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/repeat_graph copying flye/repeat_graph/repeat_graph.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/repeat_graph copying flye/repeat_graph/graph_alignment.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/repeat_graph copying flye/repeat_graph/__init__.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/repeat_graph creating /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/short_plasmids copying flye/short_plasmids/utils.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/short_plasmids copying flye/short_plasmids/unmapped_reads.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/short_plasmids copying flye/short_plasmids/plasmids.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/short_plasmids copying flye/short_plasmids/circular_sequences.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/short_plasmids copying flye/short_plasmids/__init__.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/short_plasmids creating /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/trestle copying flye/trestle/trestle_config.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/trestle copying flye/trestle/trestle.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/trestle copying flye/trestle/graph_resolver.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/trestle copying flye/trestle/divergence.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/trestle copying flye/trestle/__init__.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/trestle creating /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/tests copying flye/tests/test_toy.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/tests copying flye/tests/__init__.py -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/tests creating /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/pacbio_substitutions.mat -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/pacbio_homopolymers.mat -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/pacbio_chm13_substitutions.mat -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/pacbio_chm13_homopolymers.mat -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/nano_r94_substitutions.mat -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/nano_r94_homopolymers.mat -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/nano_r94_g36_substitutions.mat -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/nano_r94_g36_homopolymers.mat -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_subasm.cfg -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_raw_reads.cfg -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_nano_hq.cfg -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_hifi.cfg -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_defaults.cfg -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_corrected_reads.cfg -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg creating /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/tests/data copying flye/tests/data/ecoli_500kb_reads_hifi.fastq.gz -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/tests/data copying flye/tests/data/ecoli_500kb_reads.fastq.gz -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/tests/data copying flye/tests/data/ecoli_500kb.fasta -> /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/tests/data make[1]: Entering directory '/build/flye-2.9.1+dfsg' make release -C src -j 4 make[2]: Entering directory '/build/flye-2.9.1+dfsg/src' g++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG assemble/chimera.cpp -o assemble/chimera.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG assemble/extender.cpp -o assemble/extender.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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 g++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/alignment.cpp -o sequence/alignment.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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 g++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/edlib.cpp -o sequence/edlib.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/overlap.cpp -o sequence/overlap.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/sequence.cpp -o sequence/sequence.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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 g++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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 In file included from sequence/overlap.cpp:25: sequence/../common/bfcontainer.h: In instantiation of ‘BFContainer::BFIterator BFContainer::BFIterator::operator+(difference_type) [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576; difference_type = long int]’: sequence/overlap.cpp:239:43: required from here 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/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/flye-2.9.1+dfsg/lib/libcuckoo/cuckoohash_map.hh:8, from sequence/vertex_index.h:15, from sequence/vertex_index.cpp:12: /usr/include/c++/12/atomic:755:12: note: ‘struct std::atomic’ declared here 755 | struct atomic : __atomic_base | ^~~~~~~~~~~~~~~~~~~~~ sequence/../common/bfcontainer.h: In instantiation of ‘BFContainer::BFIterator BFContainer::BFIterator::operator-(difference_type) [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576; difference_type = long int]’: /usr/include/c++/12/bits/stl_algo.h:1887:71: required from ‘_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = BFContainer<{anonymous}::KmerMatch>::BFIterator; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’ /usr/include/c++/12/bits/stl_algo.h:1921:38: 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 >]’ /usr/include/c++/12/bits/stl_algo.h:1937:25: required from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = BFContainer<{anonymous}::KmerMatch>::BFIterator; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’ /usr/include/c++/12/bits/stl_algo.h:4853:18: required from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = BFContainer<{anonymous}::KmerMatch>::BFIterator; _Compare = OverlapDetector::getSeqOverlaps(const FastaRecord&, bool, OvlpDivStats&, int) const::]’ sequence/overlap.cpp:203:11: required from here 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++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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 g++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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 g++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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 g++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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 g++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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 g++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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 g++ -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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 contigger/../repeat_graph/../sequence/sequence_container.h:12, from contigger/../repeat_graph/repeat_graph.h:10, from contigger/contig_extender.h:7, from contigger/contig_extender.cpp:5: In destructor ‘DnaSequence::~DnaSequence()’, inlined from ‘void ContigExtender::generateContigs()’ at contigger/contig_extender.cpp:211:20: contigger/../repeat_graph/../sequence/sequence.h:45:34: warning: pointer used after ‘void operator delete(void*)’ [-Wuse-after-free] 45 | --_data->useCount; | ~~~~~~~^~~~~~~~ In destructor ‘DnaSequence::~DnaSequence()’, inlined from ‘void ContigExtender::generateContigs()’ at contigger/contig_extender.cpp:211:58: contigger/../repeat_graph/../sequence/sequence.h:49:40: note: call to ‘void operator delete(void*)’ here 49 | delete _data; | ^~~~~ g++ -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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++ -c -g -O2 -ffile-prefix-map=/build/flye-2.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-2.9.1+dfsg/lib/libcuckoo -I/build/flye-2.9.1+dfsg/lib/interval_tree -I/build/flye-2.9.1+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/flye-2.9.1+dfsg/bin/flye-modules -Wl,-z,relro -lz -lminimap2 -pthread -std=c++11 -rdynamic make[2]: Leaving directory '/build/flye-2.9.1+dfsg/src' make[1]: Leaving directory '/build/flye-2.9.1+dfsg' dh_auto_test -O--buildsystem=pybuild I: pybuild base:240: cd /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build; python3.11 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s OK 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:240: /usr/bin/python3 setup.py install --root /build/flye-2.9.1+dfsg/debian/flye running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py make[1]: Entering directory '/build/flye-2.9.1+dfsg' make release -C src -j 4 make[2]: Entering directory '/build/flye-2.9.1+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/flye-2.9.1+dfsg/bin/flye-modules -Wl,-z,relro -lz -lminimap2 -pthread -std=c++11 -rdynamic make[2]: Leaving directory '/build/flye-2.9.1+dfsg/src' make[1]: Leaving directory '/build/flye-2.9.1+dfsg' running install_lib creating /build/flye-2.9.1+dfsg/debian/flye/usr creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11 creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/__pycache__ copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/__pycache__/__init__.cpython-311.pyc -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/__pycache__ creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/tests creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/tests/__pycache__ copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/tests/__pycache__/test_toy.cpython-311.pyc -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/tests/__pycache__ copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/tests/__pycache__/__init__.cpython-311.pyc -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/tests/__pycache__ creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/tests/data copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/tests/data/ecoli_500kb.fasta -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/tests/data copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/tests/data/ecoli_500kb_reads.fastq.gz -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/tests/data copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/tests/data/ecoli_500kb_reads_hifi.fastq.gz -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/tests/data copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/tests/__init__.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/tests copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/tests/test_toy.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/tests creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/trestle creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/trestle/__pycache__ copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/trestle/__pycache__/__init__.cpython-311.pyc -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/trestle/__pycache__ copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/trestle/__init__.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/trestle copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/trestle/divergence.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/trestle copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/trestle/graph_resolver.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/trestle copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/trestle/trestle.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/trestle copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/trestle/trestle_config.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/trestle creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/short_plasmids creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/short_plasmids/__pycache__ copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/short_plasmids/__pycache__/__init__.cpython-311.pyc -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/short_plasmids/__pycache__ copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/short_plasmids/__init__.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/short_plasmids copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/short_plasmids/circular_sequences.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/short_plasmids copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/short_plasmids/plasmids.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/short_plasmids copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/short_plasmids/unmapped_reads.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/short_plasmids copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/short_plasmids/utils.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/short_plasmids creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/repeat_graph creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/repeat_graph/__pycache__ copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/repeat_graph/__pycache__/__init__.cpython-311.pyc -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/repeat_graph/__pycache__ copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/repeat_graph/__init__.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/repeat_graph copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/repeat_graph/graph_alignment.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/repeat_graph copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/repeat_graph/repeat_graph.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/repeat_graph creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/utils creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/utils/__pycache__ copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/utils/__pycache__/__init__.cpython-311.pyc -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/utils/__pycache__ copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/utils/__init__.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/utils copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/utils/bytes2human.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/utils copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/utils/fasta_parser.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/utils copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/utils/sam_parser.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/utils copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/utils/utils.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/utils creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/polishing creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/polishing/__pycache__ copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/polishing/__pycache__/__init__.cpython-311.pyc -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/polishing/__pycache__ copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/polishing/__init__.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/polishing copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/polishing/bubbles.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/polishing copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/polishing/consensus.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/polishing copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/polishing/polish.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/polishing copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/polishing/alignment.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/polishing creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config/__pycache__ copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/__pycache__/__init__.cpython-311.pyc -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config/__pycache__ creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config/bin_cfg copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg/asm_corrected_reads.cfg -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config/bin_cfg copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg/asm_defaults.cfg -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config/bin_cfg copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg/asm_hifi.cfg -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config/bin_cfg copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg/asm_nano_hq.cfg -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config/bin_cfg copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg/asm_raw_reads.cfg -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config/bin_cfg copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg/asm_subasm.cfg -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config/bin_cfg copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg/nano_r94_g36_homopolymers.mat -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config/bin_cfg copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg/nano_r94_g36_substitutions.mat -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config/bin_cfg copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg/nano_r94_homopolymers.mat -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config/bin_cfg copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg/nano_r94_substitutions.mat -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config/bin_cfg copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg/pacbio_chm13_homopolymers.mat -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config/bin_cfg copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg/pacbio_chm13_substitutions.mat -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config/bin_cfg copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg/pacbio_homopolymers.mat -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config/bin_cfg copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/bin_cfg/pacbio_substitutions.mat -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config/bin_cfg copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/__init__.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/configurator.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/config/py_cfg.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/assembly creating /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/assembly/__pycache__ copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/assembly/__pycache__/__init__.cpython-311.pyc -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/assembly/__pycache__ copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/assembly/__init__.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/assembly copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/assembly/assemble.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/assembly copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/assembly/repeat_graph.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/assembly copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/assembly/scaffolder.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/assembly copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/__build__.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/__init__.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/__version__.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/main.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye copying /build/flye-2.9.1+dfsg/.pybuild/cpython3_3.11/build/flye/six.py -> /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/tests/__init__.py to __init__.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/tests/test_toy.py to test_toy.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/trestle/__init__.py to __init__.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/trestle/divergence.py to divergence.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/trestle/graph_resolver.py to graph_resolver.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/trestle/trestle.py to trestle.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/trestle/trestle_config.py to trestle_config.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/short_plasmids/__init__.py to __init__.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/short_plasmids/circular_sequences.py to circular_sequences.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/short_plasmids/plasmids.py to plasmids.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/short_plasmids/unmapped_reads.py to unmapped_reads.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/short_plasmids/utils.py to utils.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/repeat_graph/__init__.py to __init__.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/repeat_graph/graph_alignment.py to graph_alignment.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/repeat_graph/repeat_graph.py to repeat_graph.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/utils/__init__.py to __init__.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/utils/bytes2human.py to bytes2human.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/utils/fasta_parser.py to fasta_parser.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/utils/sam_parser.py to sam_parser.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/utils/utils.py to utils.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/polishing/__init__.py to __init__.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/polishing/bubbles.py to bubbles.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/polishing/consensus.py to consensus.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/polishing/polish.py to polish.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/polishing/alignment.py to alignment.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config/__init__.py to __init__.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config/configurator.py to configurator.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/config/py_cfg.py to py_cfg.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/assembly/__init__.py to __init__.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/assembly/assemble.py to assemble.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/assembly/repeat_graph.py to repeat_graph.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/assembly/scaffolder.py to scaffolder.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/__build__.py to __build__.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/__init__.py to __init__.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/__version__.py to __version__.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/main.py to main.cpython-311.pyc byte-compiling /build/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye/six.py to six.cpython-311.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/flye-2.9.1+dfsg/debian/flye/usr/lib/python3.11/dist-packages/flye-2.9.1.egg-info Skipping SOURCES.txt running install_scripts Installing flye script to /build/flye-2.9.1+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/flye-2.9.1+dfsg' dh_installchangelogs docs/NEWS.md make[1]: Leaving directory '/build/flye-2.9.1+dfsg' dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild I: dh_python3 tools:114: 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_2.9.1+dfsg-1_amd64.deb'. dpkg-deb: building package 'flye-dbgsym' in '../flye-dbgsym_2.9.1+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../flye_2.9.1+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../flye_2.9.1+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: 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/1557405 and its subdirectories I: Current time: Sun Apr 30 18:02:54 -12 2023 I: pbuilder-time-stamp: 1682920974