Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/f/flye/flye_2.9+dfsg-2_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/flye-2.9+dfsg-238g17mgo/flye_2.9+dfsg-2_amd64.buildinfo Get source package info: flye=2.9+dfsg-2 Source URL: http://snapshot.notset.fr/mr/package/flye/2.9+dfsg-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1.3 autopoint=0.21-6 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6+b1 binutils=2.38-4 binutils-common=2.38-4 binutils-x86-64-linux-gnu=2.38-4 bsdextrautils=2.38-4 bsdutils=1:2.38-4 build-essential=12.9 bzip2=1.0.8-5 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.3.0-1 dash=0.5.11+git20210903+057cd650a4ed-8 debconf=1.5.79 debhelper=13.7.1 debianutils=5.7-0.2 dh-autoreconf=20 dh-python=5.20220403 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dpkg=1.21.7 dpkg-dev=1.21.7 dwz=0.14-1 file=1:5.41-4 findutils=4.9.0-3 g++=4:11.2.0-2 g++-11=11.3.0-1 gcc=4:11.2.0-2 gcc-11=11.3.0-1 gcc-11-base=11.3.0-1 gcc-12-base=12.1.0-2 gettext=0.21-6 gettext-base=0.21-6 grep=3.7-1 groff-base=1.22.4-8 gzip=1.12-1 hostname=3.23 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libamd2=1:5.12.0+dfsg-1 libarchive-zip-perl=1.68-1 libasan6=11.3.0-1 libatomic1=12.1.0-2 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libbinutils=2.38-4 libblkid1=2.38-4 libbrotli1=1.0.9-2+b3 libbz2-1.0=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libcap-ng0=0.7.9-2.2+b2 libcap2=1:2.44-1 libcc1-0=12.1.0-2 libcolamd2=1:5.12.0+dfsg-1 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-4 libctf0=2.38-4 libcurl3-gnutls=7.83.1-1+b1 libdb5.3=5.3.28+dfsg1-0.9 libdebconfclient0=0.262 libdebhelper-perl=13.7.1 libdeflate0=1.10-2 libdpkg-perl=1.21.7 libelf1=0.187-1 libexpat1=2.4.8-1 libffi8=3.4.2-4 libfile-stripnondeterminism-perl=1.13.0-1 libgcc-11-dev=11.3.0-1 libgcc-s1=12.1.0-2 libgcrypt20=1.10.1-2 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libglpk40=5.0-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.4-2 libgomp1=12.1.0-2 libgpg-error0=1.45-2 libgssapi-krb5-2=1.19.2-2+b2 libhogweed6=3.7.3-1 libhts3=1.13+ds-2+b1 libhtscodecs2=1.2.1-1 libicu71=71.1-3 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=12.1.0-2 libk5crypto3=1.19.2-2+b2 libkeyutils1=1.6.1-3 libkrb5-3=1.19.2-2+b2 libkrb5support0=1.19.2-2+b2 libldap-2.5-0=2.5.12+dfsg-1 liblemon-dev=1.3.1+dfsg-5 liblemon1.3.1=1.3.1+dfsg-5 liblsan0=12.1.0-2 libltdl7=2.4.7-4 liblz4-1=1.9.3-2 liblzma5=5.2.5-2.1 libmagic-mgc=1:5.41-4 libmagic1=1:5.41-4 libminimap2-dev=2.24+dfsg-2 libmount1=2.38-4 libmpc3=1.2.1-2 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncurses6=6.3+20220423-2 libncursesw6=6.3+20220423-2 libnettle8=3.7.3-1 libnghttp2-14=1.47.0-1+b1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.24.1-1 libpam-modules=1.4.0-13 libpam-modules-bin=1.4.0-13 libpam-runtime=1.4.0-13 libpam0g=1.4.0-13 libpcre2-8-0=10.40-1 libpcre3=2:8.39-14 libperl5.34=5.34.0-4 libpipeline1=1.5.6-1 libpsl5=0.21.0-1.2 libpython3-stdlib=3.10.4-1+b1 libpython3.10-minimal=3.10.4-4+b1 libpython3.10-stdlib=3.10.4-4+b1 libquadmath0=12.1.0-2 libreadline8=8.1.2-1.2 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.28+dfsg-5 libsasl2-modules-db=2.1.28+dfsg-5 libseccomp2=2.5.4-1 libselinux1=3.3-1+b2 libsigsegv2=2.14-1 libsmartcols1=2.38-4 libsqlite3-0=3.38.5-1 libssh2-1=1.10.0-3+b1 libssl3=3.0.3-4 libstdc++-11-dev=11.3.0-1 libstdc++6=12.1.0-2 libsub-override-perl=0.09-2 libsuitesparseconfig5=1:5.12.0+dfsg-1 libsystemd0=250.4-1 libtasn1-6=4.18.0-4 libtinfo6=6.3+20220423-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.7-4 libtsan0=11.3.0-1 libubsan1=12.1.0-2 libuchardet0=0.0.7-1 libudev1=250.4-1 libunistring2=1.0-1 libuuid1=2.38-4 libxml2=2.9.14+dfsg-1 libzstd1=1.5.2+dfsg-1 linux-libc-dev=5.17.6-1+b1 login=1:4.11.1+dfsg1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.2-1 mawk=1.3.4.20200120-3+b1 media-types=8.0.0 ncurses-base=6.3+20220423-2 ncurses-bin=6.3+20220423-2 patch=2.7.6-7 perl=5.34.0-4 perl-base=5.34.0-4 perl-modules-5.34=5.34.0-4 po-debconf=1.0.21+nmu1 python3=3.10.4-1+b1 python3-distutils=3.9.12-1 python3-lib2to3=3.9.12-1 python3-minimal=3.10.4-1+b1 python3-pkg-resources=59.6.0-1.2 python3-setuptools=59.6.0-1.2 python3.10=3.10.4-4+b1 python3.10-minimal=3.10.4-4+b1 readline-common=8.1.2-1.2 rpcsvc-proto=1.4.2-4 samtools=1.13-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.03-1 tar=1.34+dfsg-1 util-linux=2.38-4 util-linux-extra=2.38-4 xz-utils=5.2.5-2.1 zlib1g=1:1.2.11.dfsg-4 zlib1g-dev=1:1.2.11.dfsg-4 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220522T025243Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220522T025243Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220519T145256Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d flye=2.9+dfsg-2 && mkdir -p /build/flye-cP6VLR && dpkg-source --no-check -x /*.dsc /build/flye-cP6VLR/flye-2.9+dfsg && chown -R builduser:builduser /build/flye-cP6VLR" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/flye-cP6VLR/flye-2.9+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1652982477" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/flye-cP6VLR /tmp/flye-2.9+dfsg-238g17mgo bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220519T145256Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.sd6VA2c3xs as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.sd6VA2c3xs Reading package lists... Building dependency tree... util-linux is already the newest version (2.38-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 135 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220519T145256Z unstable/main amd64 libfakeroot amd64 1.28-1 [48.2 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220519T145256Z unstable/main amd64 fakeroot amd64 1.28-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 kB in 0s (1030 kB/s) Selecting previously unselected package libfakeroot: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 ... 4629 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.28-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.28-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.28-1_amd64.deb ... Unpacking fakeroot (1.28-1) ... Setting up libfakeroot:amd64 (1.28-1) ... Setting up fakeroot (1.28-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-7) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220522T025243Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220522T025243Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220519T145256Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.sd6VA2c3xs Get:1 http://snapshot.notset.fr/archive/debian/20220522T025243Z bookworm InRelease [130 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20220519T145256Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20220522T025243Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220522T025243Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220522T025243Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220522T025243Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220522T025243Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220522T025243Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20220522T025243Z bookworm/main Sources [11.9 MB] Get:4 http://snapshot.notset.fr/archive/debian/20220522T025243Z bookworm/main amd64 Packages [11.5 MB] Fetched 23.5 MB in 20s (1163 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.sd6VA2c3xs I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d flye=2.9+dfsg-2 && mkdir -p /build/flye-cP6VLR && dpkg-source --no-check -x /*.dsc /build/flye-cP6VLR/flye-2.9+dfsg && chown -R builduser:builduser /build/flye-cP6VLR"' exec /tmp/mmdebstrap.sd6VA2c3xs Reading package lists... NOTICE: 'flye' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/flye.git Please use: git clone https://salsa.debian.org/med-team/flye.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 22.8 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220522T025243Z bookworm/main flye 2.9+dfsg-2 (dsc) [2039 B] Get:2 http://snapshot.notset.fr/archive/debian/20220522T025243Z bookworm/main flye 2.9+dfsg-2 (tar) [22.8 MB] Get:3 http://snapshot.notset.fr/archive/debian/20220522T025243Z bookworm/main flye 2.9+dfsg-2 (diff) [12.7 kB] Fetched 22.8 MB in 18s (1289 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'flye_2.9+dfsg-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting flye in /build/flye-cP6VLR/flye-2.9+dfsg dpkg-source: info: unpacking flye_2.9+dfsg.orig.tar.xz dpkg-source: info: unpacking flye_2.9+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_makefile.patch dpkg-source: info: applying use_debian_packaged_libs.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/flye-cP6VLR/flye-2.9+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1652982477" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.sd6VA2c3xs dpkg-buildpackage: info: source package flye dpkg-buildpackage: info: source version 2.9+dfsg-2 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-cP6VLR/flye-2.9+dfsg' dh_auto_clean I: pybuild base:239: python3.10 setup.py clean running clean removing '/build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.10' 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-cP6VLR/flye-2.9+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:239: python3.10 setup.py config running config dh_auto_build -a -O--buildsystem=pybuild I: pybuild base:239: /usr/bin/python3 setup.py build running build running build_py creating /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye copying flye/__build__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye copying flye/__init__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye copying flye/__version__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye copying flye/main.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye copying flye/six.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye creating /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/assembly copying flye/assembly/__init__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/assembly copying flye/assembly/assemble.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/assembly copying flye/assembly/repeat_graph.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/assembly copying flye/assembly/scaffolder.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/assembly creating /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config copying flye/config/__init__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config copying flye/config/configurator.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config copying flye/config/py_cfg.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config creating /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/polishing copying flye/polishing/__init__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/polishing copying flye/polishing/bubbles.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/polishing copying flye/polishing/consensus.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/polishing copying flye/polishing/polish.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/polishing copying flye/polishing/alignment.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/polishing creating /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/utils copying flye/utils/__init__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/utils copying flye/utils/bytes2human.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/utils copying flye/utils/fasta_parser.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/utils copying flye/utils/sam_parser.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/utils copying flye/utils/utils.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/utils creating /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/repeat_graph copying flye/repeat_graph/__init__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/repeat_graph copying flye/repeat_graph/graph_alignment.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/repeat_graph copying flye/repeat_graph/repeat_graph.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/repeat_graph creating /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/short_plasmids copying flye/short_plasmids/__init__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/short_plasmids copying flye/short_plasmids/circular_sequences.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/short_plasmids copying flye/short_plasmids/plasmids.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/short_plasmids copying flye/short_plasmids/unmapped_reads.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/short_plasmids copying flye/short_plasmids/utils.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/short_plasmids creating /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/trestle copying flye/trestle/__init__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/trestle copying flye/trestle/divergence.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/trestle copying flye/trestle/graph_resolver.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/trestle copying flye/trestle/trestle.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/trestle copying flye/trestle/trestle_config.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/trestle creating /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/tests copying flye/tests/__init__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/tests copying flye/tests/test_toy.py -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/tests creating /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_corrected_reads.cfg -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_defaults.cfg -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_hifi.cfg -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_nano_hq.cfg -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_raw_reads.cfg -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_subasm.cfg -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg copying flye/config/bin_cfg/nano_r94_g36_homopolymers.mat -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg copying flye/config/bin_cfg/nano_r94_g36_substitutions.mat -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg copying flye/config/bin_cfg/nano_r94_homopolymers.mat -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg copying flye/config/bin_cfg/nano_r94_substitutions.mat -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg copying flye/config/bin_cfg/pacbio_chm13_homopolymers.mat -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg copying flye/config/bin_cfg/pacbio_chm13_substitutions.mat -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg copying flye/config/bin_cfg/pacbio_homopolymers.mat -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg copying flye/config/bin_cfg/pacbio_substitutions.mat -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg creating /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/tests/data copying flye/tests/data/ecoli_500kb.fasta -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/tests/data copying flye/tests/data/ecoli_500kb_reads.fastq.gz -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/tests/data copying flye/tests/data/ecoli_500kb_reads_hifi.fastq.gz -> /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/tests/data make[1]: Entering directory '/build/flye-cP6VLR/flye-2.9+dfsg' make release -C src -j 4 make[2]: Entering directory '/build/flye-cP6VLR/flye-2.9+dfsg/src' g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG assemble/chimera.cpp -o assemble/chimera.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG assemble/extender.cpp -o assemble/extender.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG assemble/main_assemble.cpp -o assemble/main_assemble.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG assemble/parameters_estimator.cpp -o assemble/parameters_estimator.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG sequence/alignment.cpp -o sequence/alignment.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG sequence/consensus_generator.cpp -o sequence/consensus_generator.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG sequence/edlib.cpp -o sequence/edlib.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG sequence/overlap.cpp -o sequence/overlap.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG sequence/sequence.cpp -o sequence/sequence.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG sequence/sequence_container.cpp -o sequence/sequence_container.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG sequence/vertex_index.cpp -o sequence/vertex_index.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -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+(BFContainer::BFIterator::difference_type) [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576; BFContainer::BFIterator::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/../common/bfcontainer.h: In instantiation of ‘BFContainer::BFIterator BFContainer::BFIterator::operator-(BFContainer::BFIterator::difference_type) [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576; BFContainer::BFIterator::difference_type = long int]’: /usr/include/c++/11/bits/stl_algo.h:1904:71: 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++/11/bits/stl_algo.h:1938:38: 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++/11/bits/stl_algo.h:1954:25: required from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = BFContainer<{anonymous}::KmerMatch>::BFIterator; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’ /usr/include/c++/11/bits/stl_algo.h:4875:18: 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) | ^~~~~~~~ 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-cP6VLR/flye-2.9+dfsg/lib/libcuckoo/cuckoohash_map.hh:8, from sequence/vertex_index.h:15, from sequence/vertex_index.cpp:12: /usr/include/c++/11/atomic:745:12: note: ‘struct std::atomic’ declared here 745 | struct atomic : __atomic_base | ^~~~~~~~~~~~~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG repeat_graph/haplotype_resolver.cpp -o repeat_graph/haplotype_resolver.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG repeat_graph/main_repeat.cpp -o repeat_graph/main_repeat.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG repeat_graph/multiplicity_inferer.cpp -o repeat_graph/multiplicity_inferer.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG repeat_graph/output_generator.cpp -o repeat_graph/output_generator.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG repeat_graph/read_aligner.cpp -o repeat_graph/read_aligner.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG repeat_graph/repeat_graph.cpp -o repeat_graph/repeat_graph.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG repeat_graph/repeat_resolver.cpp -o repeat_graph/repeat_resolver.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG contigger/contig_extender.cpp -o contigger/contig_extender.o g++ -c -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG contigger/main_contigger.cpp -o contigger/main_contigger.o g++ -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -c -o polishing/alignment.o polishing/alignment.cpp g++ -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -O3 -DNDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -c -o polishing/bubble_processor.o polishing/bubble_processor.cpp g++ -g -O2 -ffile-prefix-map=/build/flye-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -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-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -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-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -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-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -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-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -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-cP6VLR/flye-2.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/libcuckoo -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/interval_tree -I/build/flye-cP6VLR/flye-2.9+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -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-cP6VLR/flye-2.9+dfsg/bin/flye-modules -Wl,-z,relro -lz -lminimap2 -pthread -std=c++11 -rdynamic make[2]: Leaving directory '/build/flye-cP6VLR/flye-2.9+dfsg/src' make[1]: Leaving directory '/build/flye-cP6VLR/flye-2.9+dfsg' dh: command-omitted: The call to "dh_auto_test -a -O--buildsystem=pybuild" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install --destdir=debian/flye/ -a -O--buildsystem=pybuild I: pybuild base:239: /usr/bin/python3 setup.py install --root /build/flye-cP6VLR/flye-2.9+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-cP6VLR/flye-2.9+dfsg' make release -C src -j 4 make[2]: Entering directory '/build/flye-cP6VLR/flye-2.9+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-cP6VLR/flye-2.9+dfsg/bin/flye-modules -Wl,-z,relro -lz -lminimap2 -pthread -std=c++11 -rdynamic make[2]: Leaving directory '/build/flye-cP6VLR/flye-2.9+dfsg/src' make[1]: Leaving directory '/build/flye-cP6VLR/flye-2.9+dfsg' running install_lib creating /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr creating /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib creating /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10 creating /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages creating /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/__build__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/__init__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/__version__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/main.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/six.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye creating /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/assembly copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/assembly/__init__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/assembly copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/assembly/assemble.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/assembly copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/assembly/repeat_graph.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/assembly copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/assembly/scaffolder.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/assembly creating /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/__init__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/configurator.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/py_cfg.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config creating /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config/bin_cfg copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg/asm_corrected_reads.cfg -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config/bin_cfg copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg/asm_defaults.cfg -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config/bin_cfg copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg/asm_hifi.cfg -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config/bin_cfg copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg/asm_nano_hq.cfg -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config/bin_cfg copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg/asm_raw_reads.cfg -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config/bin_cfg copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg/asm_subasm.cfg -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config/bin_cfg copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg/nano_r94_g36_homopolymers.mat -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config/bin_cfg copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg/nano_r94_g36_substitutions.mat -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config/bin_cfg copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg/nano_r94_homopolymers.mat -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config/bin_cfg copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg/nano_r94_substitutions.mat -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config/bin_cfg copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg/pacbio_chm13_homopolymers.mat -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config/bin_cfg copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg/pacbio_chm13_substitutions.mat -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config/bin_cfg copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg/pacbio_homopolymers.mat -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config/bin_cfg copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/config/bin_cfg/pacbio_substitutions.mat -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config/bin_cfg creating /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/polishing copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/polishing/__init__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/polishing copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/polishing/bubbles.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/polishing copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/polishing/consensus.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/polishing copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/polishing/polish.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/polishing copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/polishing/alignment.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/polishing creating /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/utils copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/utils/__init__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/utils copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/utils/bytes2human.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/utils copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/utils/fasta_parser.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/utils copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/utils/sam_parser.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/utils copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/utils/utils.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/utils creating /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/repeat_graph copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/repeat_graph/__init__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/repeat_graph copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/repeat_graph/graph_alignment.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/repeat_graph copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/repeat_graph/repeat_graph.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/repeat_graph creating /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/short_plasmids copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/short_plasmids/__init__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/short_plasmids copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/short_plasmids/circular_sequences.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/short_plasmids copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/short_plasmids/plasmids.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/short_plasmids copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/short_plasmids/unmapped_reads.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/short_plasmids copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/short_plasmids/utils.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/short_plasmids creating /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/trestle copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/trestle/__init__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/trestle copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/trestle/divergence.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/trestle copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/trestle/graph_resolver.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/trestle copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/trestle/trestle.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/trestle copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/trestle/trestle_config.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/trestle creating /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/tests copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/tests/__init__.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/tests copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/tests/test_toy.py -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/tests creating /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/tests/data copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/tests/data/ecoli_500kb.fasta -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/tests/data copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/tests/data/ecoli_500kb_reads.fastq.gz -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/tests/data copying /build/flye-cP6VLR/flye-2.9+dfsg/.pybuild/cpython3_3.10/build/flye/tests/data/ecoli_500kb_reads_hifi.fastq.gz -> /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/tests/data byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/__build__.py to __build__.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/__init__.py to __init__.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/__version__.py to __version__.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/main.py to main.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/six.py to six.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/assembly/__init__.py to __init__.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/assembly/assemble.py to assemble.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/assembly/repeat_graph.py to repeat_graph.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/assembly/scaffolder.py to scaffolder.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config/__init__.py to __init__.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config/configurator.py to configurator.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/config/py_cfg.py to py_cfg.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/polishing/__init__.py to __init__.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/polishing/bubbles.py to bubbles.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/polishing/consensus.py to consensus.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/polishing/polish.py to polish.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/polishing/alignment.py to alignment.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/utils/__init__.py to __init__.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/utils/bytes2human.py to bytes2human.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/utils/fasta_parser.py to fasta_parser.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/utils/sam_parser.py to sam_parser.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/utils/utils.py to utils.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/repeat_graph/__init__.py to __init__.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/repeat_graph/graph_alignment.py to graph_alignment.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/repeat_graph/repeat_graph.py to repeat_graph.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/short_plasmids/__init__.py to __init__.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/short_plasmids/circular_sequences.py to circular_sequences.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/short_plasmids/plasmids.py to plasmids.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/short_plasmids/unmapped_reads.py to unmapped_reads.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/short_plasmids/utils.py to utils.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/trestle/__init__.py to __init__.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/trestle/divergence.py to divergence.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/trestle/graph_resolver.py to graph_resolver.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/trestle/trestle.py to trestle.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/trestle/trestle_config.py to trestle_config.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/tests/__init__.py to __init__.cpython-310.pyc byte-compiling /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye/tests/test_toy.py to test_toy.cpython-310.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-cP6VLR/flye-2.9+dfsg/debian/flye/usr/lib/python3.10/dist-packages/flye-2.9.egg-info Skipping SOURCES.txt running install_scripts Installing flye script to /build/flye-cP6VLR/flye-2.9+dfsg/debian/flye/usr/bin Installing C++ binaries dh_install -a -O--buildsystem=pybuild dh_installdocs -a -O--buildsystem=pybuild debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/flye-cP6VLR/flye-2.9+dfsg' dh_installchangelogs docs/NEWS.md make[1]: Leaving directory '/build/flye-cP6VLR/flye-2.9+dfsg' dh_installman -a -O--buildsystem=pybuild dh_python3 -a -O--buildsystem=pybuild I: dh_python3 tools:114: replacing shebang in debian/flye/usr/bin/flye dh_installsystemduser -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -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 -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild dpkg-deb: building package 'flye' in '../flye_2.9+dfsg-2_amd64.deb'. dpkg-deb: building package 'flye-dbgsym' in '../flye-dbgsym_2.9+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=any -O../flye_2.9+dfsg-2_amd64.buildinfo dpkg-genchanges --build=any -O../flye_2.9+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/flye-cP6VLR /tmp/flye-2.9+dfsg-238g17mgo I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.sd6VA2c3xs... I: success in 575.2237 seconds md5: flye-dbgsym_2.9+dfsg-2_amd64.deb: OK md5: flye_2.9+dfsg-2_amd64.deb: OK sha1: flye-dbgsym_2.9+dfsg-2_amd64.deb: OK sha1: flye_2.9+dfsg-2_amd64.deb: OK sha256: flye-dbgsym_2.9+dfsg-2_amd64.deb: OK sha256: flye_2.9+dfsg-2_amd64.deb: OK Checksums: OK