Thu Nov 21 15:40:15 UTC 2024 I: starting to build flye/unstable/amd64 on jenkins on '2024-11-21 15:40' Thu Nov 21 15:40:15 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_4/37588/console.log Thu Nov 21 15:40:15 UTC 2024 I: Downloading source for unstable/flye=2.9.5+dfsg-1 --2024-11-21 15:40:15-- http://deb.debian.org/debian/pool/main/f/flye/flye_2.9.5%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2222 (2.2K) [text/prs.lines.tag] Saving to: ‘flye_2.9.5+dfsg-1.dsc’ 0K .. 100% 319M=0s 2024-11-21 15:40:16 (319 MB/s) - ‘flye_2.9.5+dfsg-1.dsc’ saved [2222/2222] Thu Nov 21 15:40:16 UTC 2024 I: flye_2.9.5+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: flye Binary: flye Architecture: any Version: 2.9.5+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/fenderglass/Flye Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/flye Vcs-Git: https://salsa.debian.org/med-team/flye.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3, python3-setuptools, liblemon-dev, libminimap2-dev, samtools, zlib1g-dev Package-List: flye deb science optional arch=any Checksums-Sha1: c9a5034bbf5e504e50a40c9139d23aa76ec3bbb7 22759420 flye_2.9.5+dfsg.orig.tar.xz d94fb8fcb52a32541a60cde2076f2deb9e0858c0 14236 flye_2.9.5+dfsg-1.debian.tar.xz Checksums-Sha256: a638e8cbd6d8d99c852b864208fb5421afb5f07746687e587244d0207ee91807 22759420 flye_2.9.5+dfsg.orig.tar.xz b7a0ebdf9ba5080d6ed30f1a8641196901c48b1d51864881901fc6f84d5c9e24 14236 flye_2.9.5+dfsg-1.debian.tar.xz Files: 182d6fef605b75820374bd6692a17e4c 22759420 flye_2.9.5+dfsg.orig.tar.xz 8a472dabdba3eb2c15bec391be4f57e8 14236 flye_2.9.5+dfsg-1.debian.tar.xz Dgit: 5906302ad1a018c50896e22e61fb882544ca0a08 debian archive/debian/2.9.5+dfsg-1 https://git.dgit.debian.org/flye -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmbS+lYUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdohgg//YMVgi4cHgf6TKM4mIlg8dLf2LmzU pH1TsQEk5aCw8mF2fmkyiHIEPuVGxiMPD24i3BYNCB22icMjiWXGZLQ3Bq/XbX20 t7Zaz7WkW7zaR+TgUE++hg6y8vA8YHR/Y7Kc+fdstiU4i9otDTC2y11DHQel2o2Y CgUg3F4MTRCBy0kcsVbwcEFEXKPg2UI5usZvxDG5fYD/vQK7p6fKz2SxY4c9VwTW CRbICdYqs8tPj/m62qNta+y5xChYvBBmoIrylw+LGr/b5R93R6jGpzo4H5oAd2lf oIY5fIQkp8ZlQNrxFOXgOl9VL7CY3yNWruiXHshKJIqfBFxkdQwO54askci562HJ ZXsZGVDS3KOvjmDnJyOIOT4kSkJdeUNy0KyLZfu5zcLpjYErqZVK9efYi+q2kunT a8XCd14Ln8+zauvqEJBsm48ZCTk+OlVZ1w8g2qMjxLGN791LUn/VHC5hrGkdLdp/ dBH02WnfIVr+lGLCcwWraSCkQY0a9mZjaEQoxNsItwm1NZFZitoTVQdUYatQiPnB WJ2TrzctPavSKTNjQIs4HSEeOqzx8aim3bs2iTn4JZ7VOOfidnBxh+w/CayND3H0 jkyyHHAP6bpx1X3GCnJu5fY2t2k7l8F69DyyMfishJTmhdr4mWCbilmwtmOusVIX /fNTgOSpF2RdAX4= =dqzQ -----END PGP SIGNATURE----- Thu Nov 21 15:40:16 UTC 2024 I: Checking whether the package is not for us Thu Nov 21 15:40:16 UTC 2024 I: Starting 1st build on remote node ionos15-amd64.debian.net. Thu Nov 21 15:40:16 UTC 2024 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Thu Nov 21 15:43:04 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Dec 24 10:03:17 -12 2025 I: pbuilder-time-stamp: 1766613797 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [flye_2.9.5+dfsg-1.dsc] I: copying [./flye_2.9.5+dfsg.orig.tar.xz] I: copying [./flye_2.9.5+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Aug 31 11:11:18 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./flye_2.9.5+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting flye in flye-2.9.5+dfsg dpkg-source: info: unpacking flye_2.9.5+dfsg.orig.tar.xz dpkg-source: info: unpacking flye_2.9.5+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs.patch dpkg-source: info: applying cppflags.patch dpkg-source: info: applying python3.12.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3231297/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='f51e3ce56df4430da6044ffb5932144e' 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='3231297' 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.cRoMd6tT/pbuilderrc_yKXX --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.cRoMd6tT/b1 --logfile b1/build.log flye_2.9.5+dfsg-1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3231297/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3, python3-setuptools, liblemon-dev, libminimap2-dev, samtools, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19966 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on liblemon-dev; however: Package liblemon-dev is not installed. pbuilder-satisfydepends-dummy depends on libminimap2-dev; however: Package libminimap2-dev is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libamd3{a} libarchive-zip-perl{a} libbrotli1{a} libcolamd3{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglpk40{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblemon-dev{a} liblemon1.3.1{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libminimap2-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libsuitesparseconfig7{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-autocommand{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 89 newly installed, 0 to remove and 0 not upgraded. Need to get 33.4 MB of archives. After unpacking 125 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 44 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 58 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.2.0-1 [731 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20241024 [109 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libsuitesparseconfig7 amd64 1:7.8.3+dfsg-2 [23.8 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libamd3 amd64 1:7.8.3+dfsg-2 [40.7 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libcolamd3 amd64 1:7.8.3+dfsg-2 [32.5 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.4.0-1+b1 [63.6 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.11.0-1 [359 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.4.7-8 [393 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libglpk40 amd64 5.0-1+b2 [401 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 liblemon1.3.1 amd64 1.3.1+dfsg-6+b2 [55.0 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 liblemon-dev amd64 1.3.1+dfsg-6+b2 [325 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libminimap2-dev amd64 2.27+dfsg-1+b2 [131 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.20-3 [653 kB] Fetched 33.4 MB in 3s (9590 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... 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Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:amd64 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Dec 24 22:04:16 UTC 2025. Universal Time is now: Wed Dec 24 22:04:16 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libncurses6:amd64 (6.5-2+b1) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libltdl7:amd64 (2.4.7-8) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.4.0-1+b1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libsuitesparseconfig7:amd64 (1:7.8.3+dfsg-2) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:amd64 (1.6.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libamd3:amd64 (1:7.8.3+dfsg-2) ... Setting up libtool (2.4.7-8) ... Setting up libcolamd3:amd64 (1:7.8.3+dfsg-2) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libglpk40:amd64 (5.0-1+b2) ... Setting up libminimap2-dev (2.27+dfsg-1+b2) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up liblemon1.3.1:amd64 (1.3.1+dfsg-6+b2) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.11.0-1) ... Setting up liblemon-dev (1.3.1+dfsg-6+b2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up libhts3t64:amd64 (1.20+ds-2) ... Setting up libpython3.12-stdlib:amd64 (3.12.7-3) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up samtools (1.20-3) ... Setting up libpython3-stdlib:amd64 (3.12.7-1) ... Setting up python3 (3.12.7-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-setuptools (75.2.0-1) ... Setting up dh-python (6.20241024) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/flye-2.9.5+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_2.9.5+dfsg-1_source.changes dpkg-buildpackage: info: source package flye dpkg-buildpackage: info: source version 2.9.5+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/flye-2.9.5+dfsg' dh_auto_clean I: pybuild base:311: python3.12 setup.py clean running clean removing '/build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it find src -name "*.o" -delete rm -f bin/flye-modules rm -rf flye.egg-info/ make[1]: Leaving directory '/build/reproducible-path/flye-2.9.5+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye copying flye/main.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye copying flye/__build__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye copying flye/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye copying flye/__version__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/assembly copying flye/assembly/scaffolder.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/assembly copying flye/assembly/assemble.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/assembly copying flye/assembly/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/assembly copying flye/assembly/repeat_graph.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/assembly creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config copying flye/config/configurator.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config copying flye/config/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config copying flye/config/py_cfg.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing copying flye/polishing/polish.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing copying flye/polishing/bubbles.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing copying flye/polishing/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing copying flye/polishing/alignment.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing copying flye/polishing/consensus.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils copying flye/utils/sam_parser.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils copying flye/utils/bytes2human.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils copying flye/utils/utils.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils copying flye/utils/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils copying flye/utils/fasta_parser.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/repeat_graph copying flye/repeat_graph/graph_alignment.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/repeat_graph copying flye/repeat_graph/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/repeat_graph copying flye/repeat_graph/repeat_graph.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/repeat_graph creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids copying flye/short_plasmids/unmapped_reads.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids copying flye/short_plasmids/circular_sequences.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids copying flye/short_plasmids/utils.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids copying flye/short_plasmids/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids copying flye/short_plasmids/plasmids.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle copying flye/trestle/trestle.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle copying flye/trestle/graph_resolver.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle copying flye/trestle/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle copying flye/trestle/trestle_config.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle copying flye/trestle/divergence.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests copying flye/tests/test_toy.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests copying flye/tests/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/nano_r94_substitutions.mat -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/pacbio_substitutions.mat -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_subasm.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/pacbio_chm13_homopolymers.mat -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_hifi.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/nano_r94_g36_homopolymers.mat -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_defaults.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/nano_r94_homopolymers.mat -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/pacbio_homopolymers.mat -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_raw_reads.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/pacbio_chm13_substitutions.mat -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/nano_r94_g36_substitutions.mat -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_corrected_reads.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_nano_hq.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg creating /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/data copying flye/tests/data/ecoli_500kb.fasta -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/data copying flye/tests/data/ecoli_500kb_reads.fastq.gz -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/data copying flye/tests/data/ecoli_500kb_reads_hifi.fastq.gz -> /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/data /build/reproducible-path/flye-2.9.5+dfsg/setup.py:35: DeprecationWarning: Use shutil.which instead of find_executable if not find_executable("make"): make[1]: Entering directory '/build/reproducible-path/flye-2.9.5+dfsg' make release -C src -j 4 make[2]: Entering directory '/build/reproducible-path/flye-2.9.5+dfsg/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG assemble/chimera.cpp -o assemble/chimera.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG assemble/extender.cpp -o assemble/extender.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG assemble/main_assemble.cpp -o assemble/main_assemble.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG assemble/parameters_estimator.cpp -o assemble/parameters_estimator.o assemble/main_assemble.cpp:214:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 214 | Logger::get().debug() << "Build date: " << __DATE__ << " " << __TIME__; | ^~~~~~~~ assemble/main_assemble.cpp:214:71: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 214 | Logger::get().debug() << "Build date: " << __DATE__ << " " << __TIME__; | ^~~~~~~~ In file included from assemble/../sequence/overlap.h:12, from assemble/chimera.h:7, from assemble/chimera.cpp:14: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ In file included from assemble/../sequence/overlap.h:12, from assemble/main_assemble.cpp:14: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ In file included from assemble/../sequence/overlap.h:12, from assemble/extender.h:10, from assemble/extender.cpp:14: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/alignment.cpp -o sequence/alignment.o In file included from sequence/overlap.h:12, from sequence/alignment.h:7, from sequence/alignment.cpp:8: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/consensus_generator.cpp -o sequence/consensus_generator.o In file included from sequence/../sequence/overlap.h:12, from sequence/consensus_generator.h:12, from sequence/consensus_generator.cpp:9: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/edlib.cpp -o sequence/edlib.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/overlap.cpp -o sequence/overlap.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/sequence.cpp -o sequence/sequence.o In file included from sequence/overlap.h:12, from sequence/overlap.cpp:19: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/sequence_container.cpp -o sequence/sequence_container.o In file included from sequence/overlap.cpp:25: sequence/../common/bfcontainer.h: In instantiation of ‘BFContainer::BFIterator BFContainer::BFIterator::operator+(difference_type) const [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576; difference_type = long int]’: sequence/overlap.cpp:240:43: required from here 240 | matchesList.assign(vecMatches.begin() + extRangeBegin, | ^~~~~~~~~~~~~ sequence/../common/bfcontainer.h:182:30: warning: implicitly-declared ‘constexpr BFContainer<{anonymous}::KmerMatch>::BFIterator::BFIterator(const BFContainer<{anonymous}::KmerMatch>::BFIterator&)’ is deprecated [-Wdeprecated-copy] 182 | auto tmp = *this; | ^~~ sequence/../common/bfcontainer.h:141:21: note: because ‘BFContainer<{anonymous}::KmerMatch>::BFIterator’ has user-provided ‘BFContainer::BFIterator& BFContainer::BFIterator::operator=(const BFContainer::BFIterator&) [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576]’ 141 | BFIterator& operator=(const BFIterator &rhs) | ^~~~~~~~ sequence/../common/bfcontainer.h:183:39: warning: implicitly-declared ‘constexpr BFContainer<{anonymous}::KmerMatch>::BFIterator::BFIterator(const BFContainer<{anonymous}::KmerMatch>::BFIterator&)’ is deprecated [-Wdeprecated-copy] 183 | return tmp += n; | ^ sequence/../common/bfcontainer.h:141:21: note: because ‘BFContainer<{anonymous}::KmerMatch>::BFIterator’ has user-provided ‘BFContainer::BFIterator& BFContainer::BFIterator::operator=(const BFContainer::BFIterator&) [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576]’ 141 | BFIterator& operator=(const BFIterator &rhs) | ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/vertex_index.cpp -o sequence/vertex_index.o sequence/../common/bfcontainer.h: In instantiation of ‘BFContainer::BFIterator BFContainer::BFIterator::operator-(difference_type) const [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576; difference_type = long int]’: /usr/include/c++/14/bits/stl_algo.h:1855:71: required from ‘_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = BFContainer<{anonymous}::KmerMatch>::BFIterator; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’ 1855 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, | ~~~~~~~^~~ /usr/include/c++/14/bits/stl_algo.h:1889:38: required from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = BFContainer<{anonymous}::KmerMatch>::BFIterator; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’ 1889 | std::__unguarded_partition_pivot(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1905:25: required from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = BFContainer<{anonymous}::KmerMatch>::BFIterator; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’ 1905 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1906 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1907 | __comp); | ~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:4804:18: required from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = BFContainer<{anonymous}::KmerMatch>::BFIterator; _Compare = OverlapDetector::getSeqOverlaps(const FastaRecord&, bool, OvlpDivStats&, int) const::]’ 4804 | std::__sort(__first, __last, __gnu_cxx::__ops::__iter_comp_iter(__comp)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence/overlap.cpp:204:11: required from here 204 | std::sort(vecMatches.begin(), vecMatches.end(), | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 | [](const KmerMatch& k1, const KmerMatch& k2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 206 | {return k1.extId != k2.extId ? k1.extId < k2.extId : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 207 | k1.curPos < k2.curPos;}); | ~~~~~~~~~~~~~~~~~~~~~~~~ sequence/../common/bfcontainer.h:193:30: warning: implicitly-declared ‘constexpr BFContainer<{anonymous}::KmerMatch>::BFIterator::BFIterator(const BFContainer<{anonymous}::KmerMatch>::BFIterator&)’ is deprecated [-Wdeprecated-copy] 193 | auto tmp = *this; | ^~~ sequence/../common/bfcontainer.h:141:21: note: because ‘BFContainer<{anonymous}::KmerMatch>::BFIterator’ has user-provided ‘BFContainer::BFIterator& BFContainer::BFIterator::operator=(const BFContainer::BFIterator&) [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576]’ 141 | BFIterator& operator=(const BFIterator &rhs) | ^~~~~~~~ sequence/../common/bfcontainer.h:194:39: warning: implicitly-declared ‘constexpr BFContainer<{anonymous}::KmerMatch>::BFIterator::BFIterator(const BFContainer<{anonymous}::KmerMatch>::BFIterator&)’ is deprecated [-Wdeprecated-copy] 194 | return tmp -= n; | ^ sequence/../common/bfcontainer.h:141:21: note: because ‘BFContainer<{anonymous}::KmerMatch>::BFIterator’ has user-provided ‘BFContainer::BFIterator& BFContainer::BFIterator::operator=(const BFContainer::BFIterator&) [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576]’ 141 | BFIterator& operator=(const BFIterator &rhs) | ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/graph_processing.cpp -o repeat_graph/graph_processing.o sequence/vertex_index.cpp: In member function ‘void KmerCounter::count(bool)’: sequence/vertex_index.cpp:380:28: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::atomic’ with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess] 380 | std::memset(_flatCounter, 0, COUNTER_LEN); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo/cuckoohash_map.hh:8, from sequence/vertex_index.h:15, from sequence/vertex_index.cpp:12: /usr/include/c++/14/atomic:758:12: note: ‘struct std::atomic’ declared here 758 | struct atomic : __atomic_base | ^~~~~~~~~~~~~~~~~~~~~ In file included from repeat_graph/../sequence/overlap.h:12, from repeat_graph/repeat_graph.h:11, from repeat_graph/graph_processing.h:10, from repeat_graph/graph_processing.cpp:7: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/haplotype_resolver.cpp -o repeat_graph/haplotype_resolver.o In file included from repeat_graph/../sequence/overlap.h:12, from repeat_graph/repeat_graph.h:11, from repeat_graph/haplotype_resolver.h:7, from repeat_graph/haplotype_resolver.cpp:1: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/main_repeat.cpp -o repeat_graph/main_repeat.o repeat_graph/main_repeat.cpp:152:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 152 | Logger::get().debug() << "Build date: " << __DATE__ << " " << __TIME__; | ^~~~~~~~ repeat_graph/main_repeat.cpp:152:71: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 152 | Logger::get().debug() << "Build date: " << __DATE__ << " " << __TIME__; | ^~~~~~~~ In file included from repeat_graph/../repeat_graph/../sequence/overlap.h:12, from repeat_graph/../repeat_graph/repeat_graph.h:11, from repeat_graph/main_repeat.cpp:17: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/multiplicity_inferer.cpp -o repeat_graph/multiplicity_inferer.o In file included from repeat_graph/../sequence/overlap.h:12, from repeat_graph/repeat_graph.h:11, from repeat_graph/multiplicity_inferer.h:7, from repeat_graph/multiplicity_inferer.cpp:5: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/output_generator.cpp -o repeat_graph/output_generator.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/read_aligner.cpp -o repeat_graph/read_aligner.o In file included from repeat_graph/../sequence/overlap.h:12, from repeat_graph/repeat_graph.h:11, from repeat_graph/output_generator.h:13, from repeat_graph/output_generator.cpp:5: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/repeat_graph.cpp -o repeat_graph/repeat_graph.o In file included from repeat_graph/../sequence/overlap.h:12, from repeat_graph/repeat_graph.h:11, from repeat_graph/read_aligner.h:11, from repeat_graph/read_aligner.cpp:5: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ In file included from repeat_graph/../sequence/overlap.h:12, from repeat_graph/repeat_graph.cpp:9: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/repeat_resolver.cpp -o repeat_graph/repeat_resolver.o In file included from repeat_graph/../sequence/overlap.h:12, from repeat_graph/repeat_graph.h:11, from repeat_graph/repeat_resolver.h:11, from repeat_graph/repeat_resolver.cpp:8: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG contigger/contig_extender.cpp -o contigger/contig_extender.o In file included from contigger/../repeat_graph/../sequence/overlap.h:12, from contigger/../repeat_graph/repeat_graph.h:11, from contigger/contig_extender.h:7, from contigger/contig_extender.cpp:5: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG contigger/main_contigger.cpp -o contigger/main_contigger.o contigger/main_contigger.cpp:159:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 159 | Logger::get().debug() << "Build date: " << __DATE__ << " " << __TIME__; | ^~~~~~~~ contigger/main_contigger.cpp:159:71: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 159 | Logger::get().debug() << "Build date: " << __DATE__ << " " << __TIME__; | ^~~~~~~~ In file included from contigger/../repeat_graph/../sequence/overlap.h:12, from contigger/../repeat_graph/repeat_graph.h:11, from contigger/main_contigger.cpp:18: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 71 | IntervalTree(const intervalTree& other) | ^ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:71:22: note: remove the ‘< >’ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 91 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -c -o polishing/alignment.o polishing/alignment.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -c -o polishing/bubble_processor.o polishing/bubble_processor.cpp In file included from polishing/bubble_processor.cpp:9: polishing/bubble_processor.h: In constructor ‘BubbleProcessor::BubbleProcessor(const std::string&, const std::string&, bool, bool)’: polishing/bubble_processor.h:48:35: warning: ‘BubbleProcessor::_dinucFixer’ will be initialized after [-Wreorder] 48 | const DinucleotideFixer _dinucFixer; | ^~~~~~~~~~~ polishing/bubble_processor.h:40:51: warning: ‘bool BubbleProcessor::_verbose’ [-Wreorder] 40 | bool _verbose; | ^~~~~~~~ polishing/bubble_processor.cpp:21:1: warning: when initialized here [-Wreorder] 21 | BubbleProcessor::BubbleProcessor(const std::string& subsMatPath, | ^~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -c -o polishing/dinucleotide_fixer.o polishing/dinucleotide_fixer.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -c -o polishing/general_polisher.o polishing/general_polisher.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -c -o polishing/homo_polisher.o polishing/homo_polisher.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -c -o polishing/main_polisher.o polishing/main_polisher.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -c -o polishing/subs_matrix.o polishing/subs_matrix.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG main.cpp -o main.o g++ assemble/chimera.o assemble/extender.o assemble/main_assemble.o assemble/parameters_estimator.o sequence/alignment.o sequence/consensus_generator.o sequence/edlib.o sequence/overlap.o sequence/sequence.o sequence/sequence_container.o sequence/vertex_index.o repeat_graph/graph_processing.o repeat_graph/haplotype_resolver.o repeat_graph/main_repeat.o repeat_graph/multiplicity_inferer.o repeat_graph/output_generator.o repeat_graph/read_aligner.o repeat_graph/repeat_graph.o repeat_graph/repeat_resolver.o contigger/contig_extender.o contigger/main_contigger.o polishing/alignment.o polishing/bubble_processor.o polishing/dinucleotide_fixer.o polishing/general_polisher.o polishing/homo_polisher.o polishing/main_polisher.o polishing/subs_matrix.o main.o -o /build/reproducible-path/flye-2.9.5+dfsg/bin/flye-modules -Wl,-z,relro -Wl,-z,now -lz -lminimap2 -pthread -std=c++11 -rdynamic make[2]: Leaving directory '/build/reproducible-path/flye-2.9.5+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/flye-2.9.5+dfsg' dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build; python3.12 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/flye/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/flye-2.9.5+dfsg/debian/flye running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py /build/reproducible-path/flye-2.9.5+dfsg/setup.py:35: DeprecationWarning: Use shutil.which instead of find_executable if not find_executable("make"): make[1]: Entering directory '/build/reproducible-path/flye-2.9.5+dfsg' make release -C src -j 4 make[2]: Entering directory '/build/reproducible-path/flye-2.9.5+dfsg/src' g++ assemble/chimera.o assemble/extender.o assemble/main_assemble.o assemble/parameters_estimator.o sequence/alignment.o sequence/consensus_generator.o sequence/edlib.o sequence/overlap.o sequence/sequence.o sequence/sequence_container.o sequence/vertex_index.o repeat_graph/graph_processing.o repeat_graph/haplotype_resolver.o repeat_graph/main_repeat.o repeat_graph/multiplicity_inferer.o repeat_graph/output_generator.o repeat_graph/read_aligner.o repeat_graph/repeat_graph.o repeat_graph/repeat_resolver.o contigger/contig_extender.o contigger/main_contigger.o polishing/alignment.o polishing/bubble_processor.o polishing/dinucleotide_fixer.o polishing/general_polisher.o polishing/homo_polisher.o polishing/main_polisher.o polishing/subs_matrix.o main.o -o /build/reproducible-path/flye-2.9.5+dfsg/bin/flye-modules -Wl,-z,relro -Wl,-z,now -lz -lminimap2 -pthread -std=c++11 -rdynamic make[2]: Leaving directory '/build/reproducible-path/flye-2.9.5+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/flye-2.9.5+dfsg' running install_lib creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing/polish.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing/bubbles.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing/alignment.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/polishing/consensus.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/main.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils/sam_parser.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils/bytes2human.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils/utils.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/utils/fasta_parser.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/test_toy.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/__pycache__/test_toy.cpython-312.pyc -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests/__pycache__ creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests/data copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/data/ecoli_500kb.fasta -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests/data copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/data/ecoli_500kb_reads.fastq.gz -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests/data copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/data/ecoli_500kb_reads_hifi.fastq.gz -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests/data copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/tests/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/__build__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle/trestle.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle/graph_resolver.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle/trestle_config.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/trestle/divergence.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/assembly/scaffolder.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/assembly/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/assembly/assemble.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/assembly/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/assembly/repeat_graph.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids/unmapped_reads.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids/circular_sequences.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids/utils.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/short_plasmids/plasmids.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/configurator.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/nano_r94_substitutions.mat -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/pacbio_substitutions.mat -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/asm_subasm.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/pacbio_chm13_homopolymers.mat -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/asm_hifi.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/nano_r94_g36_homopolymers.mat -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/asm_defaults.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/nano_r94_homopolymers.mat -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/pacbio_homopolymers.mat -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/asm_raw_reads.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/pacbio_chm13_substitutions.mat -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/nano_r94_g36_substitutions.mat -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/asm_corrected_reads.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/bin_cfg/asm_nano_hq.cfg -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/bin_cfg copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/config/py_cfg.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/__version__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/repeat_graph creating /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/repeat_graph/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/repeat_graph/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/repeat_graph/__pycache__ copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/repeat_graph/graph_alignment.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/repeat_graph copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/repeat_graph/__init__.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/repeat_graph copying /build/reproducible-path/flye-2.9.5+dfsg/.pybuild/cpython3_3.12/build/flye/repeat_graph/repeat_graph.py -> /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/repeat_graph byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing/polish.py to polish.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing/bubbles.py to bubbles.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing/alignment.py to alignment.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/polishing/consensus.py to consensus.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/main.py to main.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils/sam_parser.py to sam_parser.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils/bytes2human.py to bytes2human.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils/utils.py to utils.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/utils/fasta_parser.py to fasta_parser.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests/test_toy.py to test_toy.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/tests/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/__build__.py to __build__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle/trestle.py to trestle.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle/graph_resolver.py to graph_resolver.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle/trestle_config.py to trestle_config.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/trestle/divergence.py to divergence.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly/scaffolder.py to scaffolder.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly/assemble.py to assemble.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/assembly/repeat_graph.py to repeat_graph.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids/unmapped_reads.py to unmapped_reads.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids/circular_sequences.py to circular_sequences.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids/utils.py to utils.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/short_plasmids/plasmids.py to plasmids.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/configurator.py to configurator.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/config/py_cfg.py to py_cfg.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/__version__.py to __version__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/repeat_graph/graph_alignment.py to graph_alignment.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/repeat_graph/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye/repeat_graph/repeat_graph.py to repeat_graph.cpython-312.pyc running install_egg_info running egg_info creating flye.egg-info writing flye.egg-info/PKG-INFO writing dependency_links to flye.egg-info/dependency_links.txt writing entry points to flye.egg-info/entry_points.txt writing top-level names to flye.egg-info/top_level.txt writing manifest file 'flye.egg-info/SOURCES.txt' reading manifest file 'flye.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'flye.egg-info/SOURCES.txt' Copying flye.egg-info to /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/lib/python3.12/dist-packages/flye-2.9.5.egg-info Skipping SOURCES.txt running install_scripts Installing flye script to /build/reproducible-path/flye-2.9.5+dfsg/debian/flye/usr/bin Installing C++ binaries dh_install -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/flye-2.9.5+dfsg' dh_installchangelogs docs/NEWS.md make[1]: Leaving directory '/build/reproducible-path/flye-2.9.5+dfsg' dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild I: dh_python3 tools:113: replacing shebang in debian/flye/usr/bin/flye dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'flye-dbgsym' in '../flye-dbgsym_2.9.5+dfsg-1_amd64.deb'. dpkg-deb: building package 'flye' in '../flye_2.9.5+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../flye_2.9.5+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../flye_2.9.5+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: 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/3231297 and its subdirectories I: Current time: Wed Dec 24 10:06:02 -12 2025 I: pbuilder-time-stamp: 1766613962 Thu Nov 21 15:43:04 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Thu Nov 21 15:43:04 UTC 2024 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Thu Nov 21 15:46:31 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Thu Nov 21 15:46:31 UTC 2024 I: flye_2.9.5+dfsg-1_amd64.changes: Format: 1.8 Date: Sat, 31 Aug 2024 12:43:43 +0200 Source: flye Binary: flye flye-dbgsym Architecture: amd64 Version: 2.9.5+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: flye - de novo assembler for single molecule sequencing reads using repe Changes: flye (2.9.5+dfsg-1) unstable; urgency=medium . * New upstream version 2.9.5+dfsg * python3.12.patch: unfuzz. * python3.12.patch: forwarding not needed. This is because most of the changes are vendoring removal; upstream did move to Python 3.12 in the present version. Checksums-Sha1: 9b746ace1a826aa95ce691e6de6f3ca22def3382 11959220 flye-dbgsym_2.9.5+dfsg-1_amd64.deb 31fe52cde9f8ff5887d2825525c70b30aac0bfd3 7106 flye_2.9.5+dfsg-1_amd64.buildinfo 8567bd98d5c08234b87123a6d65a668efe4716c9 23203780 flye_2.9.5+dfsg-1_amd64.deb Checksums-Sha256: a253ff8528ec43ee0b6f474858946bb9837a9653750c849db48698f2c5f97ba8 11959220 flye-dbgsym_2.9.5+dfsg-1_amd64.deb da14d9b374e830525a576b5704067a6d820ba4944f9f119e7fd53a3394190091 7106 flye_2.9.5+dfsg-1_amd64.buildinfo b821979c594f232348a566efc65f5c1f8acf444fb36f009229c8c9fde9971862 23203780 flye_2.9.5+dfsg-1_amd64.deb Files: eb2903d6956a3ef55a8a656903a6af72 11959220 debug optional flye-dbgsym_2.9.5+dfsg-1_amd64.deb c2afffdafa5df75fc3c9f24cf79ebcaf 7106 science optional flye_2.9.5+dfsg-1_amd64.buildinfo a6977ad0993d9d0df71190fbc4a42ae6 23203780 science optional flye_2.9.5+dfsg-1_amd64.deb Thu Nov 21 15:46:32 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_4-37588.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.cRoMd6tT/flye_2.9.5+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.cRoMd6tT/flye_2.9.5+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.cRoMd6tT/flye_2.9.5+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.cRoMd6tT/b1/flye_2.9.5+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.cRoMd6tT/b2/flye_2.9.5+dfsg-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.635s) 0.635s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.318s) 0.318s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 928ms CPU time consumed: 925ms Thu Nov 21 15:46:34 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Thu Nov 21 15:46:34 UTC 2024 I: flye from unstable built successfully and reproducibly on amd64. Thu Nov 21 15:46:35 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Nov 21 15:46:35 UTC 2024 I: Submitting 8.0K b1/flye_2.9.5+dfsg-1_amd64.buildinfo.asc Thu Nov 21 15:46:35 UTC 2024 I: Submitting 8.0K b2/flye_2.9.5+dfsg-1_amd64.buildinfo.asc Thu Nov 21 15:46:36 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Nov 21 15:46:36 UTC 2024 I: Done submitting .buildinfo files. Thu Nov 21 15:46:36 UTC 2024 I: Removing signed flye_2.9.5+dfsg-1_amd64.buildinfo.asc files: removed './b1/flye_2.9.5+dfsg-1_amd64.buildinfo.asc' removed './b2/flye_2.9.5+dfsg-1_amd64.buildinfo.asc'