I: pbuilder: network access will be disabled during build I: Current time: Mon Dec 30 22:39:35 +14 2024 I: pbuilder-time-stamp: 1735547975 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 [jellyfish_2.3.1-4.dsc] I: copying [./jellyfish_2.3.1.orig.tar.gz] I: copying [./jellyfish_2.3.1-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./jellyfish_2.3.1-4.dsc: unsupported subcommand dpkg-source: info: extracting jellyfish in jellyfish-2.3.1 dpkg-source: info: unpacking jellyfish_2.3.1.orig.tar.gz dpkg-source: info: unpacking jellyfish_2.3.1-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying drop_distutils dpkg-source: info: applying manpage_whatis_entry.patch dpkg-source: info: applying portability.patch dpkg-source: info: applying test_needs_bash dpkg-source: info: applying python3 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3884382/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Dec 30 08:39 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3884382/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3884382/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=3c580a83566f4de19d5cf12a9d4099b6 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3884382 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.S8ydirpp/pbuilderrc_ab9b --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.S8ydirpp/b2 --logfile b2/build.log jellyfish_2.3.1-4.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3884382/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: arm64 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), architecture-is-little-endian, architecture-is-64-bit, d-shlibs, autoconf-archive, yaggo, pkgconf, bc, time, procps, swig, python3-all-dev, dh-sequence-python3, python3-setuptools, perl, chrpath, libhts-dev, dos2unix, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19976 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 architecture-is-little-endian; however: Package architecture-is-little-endian is not installed. pbuilder-satisfydepends-dummy depends on architecture-is-64-bit; however: Package architecture-is-64-bit is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on autoconf-archive; however: Package autoconf-archive is not installed. pbuilder-satisfydepends-dummy depends on yaggo; however: Package yaggo is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on bc; however: Package bc is not installed. pbuilder-satisfydepends-dummy depends on time; however: Package time is not installed. pbuilder-satisfydepends-dummy depends on procps; however: Package procps is not installed. pbuilder-satisfydepends-dummy depends on swig; however: Package swig is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev 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-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on dos2unix; however: Package dos2unix is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools 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: architecture-properties{a} autoconf{a} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bc{a} bsdextrautils{a} ca-certificates{a} chrpath{a} comerr-dev{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dos2unix{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-2.5-0{a} libldap-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libnsl2{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librtmp-dev{a} librtmp1{a} libruby{a} libruby3.1t64{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6{a} libtasn1-6-dev{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2{a} libyaml-0-2{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} netbase{a} nettle-dev{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-dev{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-dev{a} python3.12-minimal{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} rake{a} readline-common{a} ruby{a} ruby-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} samtools{a} sensible-utils{a} swig{a} time{a} tzdata{a} yaggo{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl fonts-lato javascript-common krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc linux-sysctl-defaults lynx psmisc publicsuffix wget zip 0 packages upgraded, 169 newly installed, 0 to remove and 0 not upgraded. Need to get 79.8 MB of archives. After unpacking 336 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.8-3 [810 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.8-3 [1941 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.8-1 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024b-4 [256 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2~rc1-2 [23.7 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 14 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.8-3 [1906 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.8-3 [677 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.8-1 [9788 B] Get: 24 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.8-1 [27.9 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.1-2 [852 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.1-2 [1987 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-6 [872 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.3.2-2 [1347 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20241223 [164 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-3 [198 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-13 [91.4 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 architecture-properties arm64 0.2.3 [2184 B] Get: 42 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-3 [723 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 bc arm64 1.07.1-4+b1 [101 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 chrpath arm64 0.18-1 [13.2 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 comerr-dev arm64 2.1-1.47.2~rc1-2 [55.7 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 d-shlibs all 0.109 [11.1 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.23 [90.6 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 57 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-3 [1532 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.23 [919 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 72 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 75.6.0-1 [720 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20241217 [113 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 dos2unix arm64 7.5.2-1+b1 [516 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libgssrpc4t64 arm64 1.21.3-3 [56.7 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libkadm5clnt-mit12 arm64 1.21.3-3 [40.3 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libkdb5-10t64 arm64 1.21.3-3 [40.8 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libkadm5srv-mit12 arm64 1.21.3-3 [52.2 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 krb5-multidev arm64 1.21.3-3 [126 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.19.0-3+b3 [46.9 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.8-2 [1363 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.19+dfsg-1 [175 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.6.0-2 [60.5 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.9.1-1 [109 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.9.1-1 [17.3 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.11.1-1 [332 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libunbound8 arm64 1.22.0-1 [553 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libgnutls-dane0t64 arm64 3.8.8-2 [446 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libgnutls-openssl27t64 arm64 3.8.8-2 [446 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libp11-kit-dev arm64 0.25.5-3 [208 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libtasn1-6-dev arm64 4.19.0-3+b3 [96.5 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-3 [329 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-3 [621 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libgnutls28-dev arm64 3.8.8-2 [1404 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libkrb5-dev arm64 1.21.3-3 [15.8 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libldap-dev arm64 2.5.19+dfsg-1 [300 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libnghttp3-dev arm64 1.6.0-2 [86.5 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.9.1-1 [23.0 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libngtcp2-dev arm64 1.9.1-1 [162 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.3.2-2 [3185 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libzstd-dev arm64 1.5.6+dfsg-1+b1 [329 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libcurl4-gnutls-dev arm64 8.11.1-1 [461 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libdeflate-dev arm64 1.22-1 [51.2 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20240808-1 [89.2 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 liblzma-dev arm64 5.6.3-1+b1 [312 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 libhts-dev arm64 1.20+ds-2 [1626 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 8.1.3-3 [30.4 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libpython3.12t64 arm64 3.12.8-3 [1983 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libpython3.12-dev arm64 3.12.8-3 [4823 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.12.8-1 [10.1 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.1-2 [1913 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libpython3.13 arm64 3.13.1-2 [1971 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libpython3.13-dev arm64 3.13.1-2 [4709 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libpython3-all-dev arm64 3.12.8-1 [1068 B] Get: 148 http://deb.debian.org/debian unstable/main arm64 rubygems-integration all 1.18 [6704 B] Get: 149 http://deb.debian.org/debian unstable/main arm64 ruby3.1 arm64 3.1.2-8.4 [664 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 ruby arm64 1:3.1+nmu1 [5584 B] Get: 152 http://deb.debian.org/debian unstable/main arm64 rake all 13.2.1-1 [65.2 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 ruby-sdbm arm64 1.0.0-5+b5 [14.6 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-2 [49.2 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 libruby3.1t64 arm64 3.1.2-8.4 [5266 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libruby arm64 1:3.1+nmu1 [4664 B] Get: 160 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.1-2 [740 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.12.8-1 [1048 B] Get: 162 http://deb.debian.org/debian unstable/main arm64 python3.12-dev arm64 3.12.8-3 [505 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.12.8-1 [26.1 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 python3.13-dev arm64 3.13.1-2 [504 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 python3-all-dev arm64 3.12.8-1 [1068 B] Get: 166 http://deb.debian.org/debian unstable/main arm64 samtools arm64 1.20-3+b1 [629 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 swig arm64 4.3.0-0.1 [1406 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 time arm64 1.9-0.2+b1 [48.1 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 yaggo all 1.5.11-2 [21.4 kB] Fetched 79.8 MB in 1s (131 MB/s) Preconfiguring packages ... Selecting previously unselected package autoconf-archive. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19976 files and directories currently installed.) Preparing to unpack .../autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package libpython3.12-minimal:arm64. Preparing to unpack .../libpython3.12-minimal_3.12.8-3_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.8-3) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.8-3_arm64.deb ... Unpacking python3.12-minimal (3.12.8-3) ... Setting up libpython3.12-minimal:arm64 (3.12.8-3) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21478 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.8-1_arm64.deb ... Unpacking python3-minimal (3.12.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... 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Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../09-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../10-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../11-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../12-libtirpc3t64_1.3.4+ds-1.3+b1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../13-libnsl2_1.3.0-3+b3_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../14-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../15-libreadline8t64_8.2-6_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../16-libpython3.12-stdlib_3.12.8-3_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.8-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../17-python3.12_3.12.8-3_arm64.deb ... Unpacking python3.12 (3.12.8-3) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../18-libpython3-stdlib_3.12.8-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.8-1) ... Setting up python3-minimal (3.12.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 22546 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.8-1_arm64.deb ... Unpacking python3 (3.12.8-1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../001-libpython3.13-minimal_3.13.1-2_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.1-2) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../002-python3.13-minimal_3.13.1-2_arm64.deb ... Unpacking python3.13-minimal (3.13.1-2) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../003-libproc2-0_2%3a4.0.4-6_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../004-procps_2%3a4.0.4-6_arm64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../005-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../006-openssl_3.3.2-2_arm64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../007-ca-certificates_20241223_all.deb ... Unpacking ca-certificates (20241223) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../008-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../009-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../010-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../011-gettext-base_0.22.5-3_arm64.deb ... Unpacking gettext-base (0.22.5-3) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../012-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../013-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../014-bsdextrautils_2.40.2-13_arm64.deb ... Unpacking bsdextrautils (2.40.2-13) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../015-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../016-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package architecture-properties:arm64. Preparing to unpack .../017-architecture-properties_0.2.3_arm64.deb ... Unpacking architecture-properties:arm64 (0.2.3) ... Selecting previously unselected package m4. Preparing to unpack .../018-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../019-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../020-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../021-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../022-autopoint_0.22.5-3_all.deb ... Unpacking autopoint (0.22.5-3) ... Selecting previously unselected package bc. Preparing to unpack .../023-bc_1.07.1-4+b1_arm64.deb ... Unpacking bc (1.07.1-4+b1) ... Selecting previously unselected package chrpath. Preparing to unpack .../024-chrpath_0.18-1_arm64.deb ... Unpacking chrpath (0.18-1) ... Selecting previously unselected package comerr-dev:arm64. Preparing to unpack .../025-comerr-dev_2.1-1.47.2~rc1-2_arm64.deb ... Unpacking comerr-dev:arm64 (2.1-1.47.2~rc1-2) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../026-d-shlibs_0.109_all.deb ... Unpacking d-shlibs (0.109) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../027-libdebhelper-perl_13.23_all.deb ... Unpacking libdebhelper-perl (13.23) ... Selecting previously unselected package libtool. Preparing to unpack .../028-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../029-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../030-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../031-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 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Selecting previously unselected package python3.13-dev. Preparing to unpack .../140-python3.13-dev_3.13.1-2_arm64.deb ... Unpacking python3.13-dev (3.13.1-2) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../141-python3-all-dev_3.12.8-1_arm64.deb ... Unpacking python3-all-dev (3.12.8-1) ... Selecting previously unselected package samtools. Preparing to unpack .../142-samtools_1.20-3+b1_arm64.deb ... Unpacking samtools (1.20-3+b1) ... Selecting previously unselected package swig. Preparing to unpack .../143-swig_4.3.0-0.1_arm64.deb ... Unpacking swig (4.3.0-0.1) ... Selecting previously unselected package time. Preparing to unpack .../144-time_1.9-0.2+b1_arm64.deb ... Unpacking time (1.9-0.2+b1) ... Selecting previously unselected package yaggo. Preparing to unpack .../145-yaggo_1.5.11-2_all.deb ... Unpacking yaggo (1.5.11-2) ... Setting up libhtscodecs2:arm64 (1.6.1-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up time (1.9-0.2+b1) ... Setting up libkeyutils1:arm64 (1.6.3-4) ... Setting up swig (4.3.0-0.1) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up libzstd-dev:arm64 (1.5.6+dfsg-1+b1) ... Setting up bsdextrautils (2.40.2-13) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.5-2) ... Setting up architecture-properties:arm64 (0.2.3) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.23) ... Setting up libbrotli1:arm64 (1.1.0-2+b6) ... Setting up libedit2:arm64 (3.1-20240808-1) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up libnghttp2-14:arm64 (1.64.0-1) ... Setting up libdeflate0:arm64 (1.22-1) ... Setting up gettext-base (0.22.5-3) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up autoconf-archive (20220903-3) ... Setting up libcom-err2:arm64 (1.47.2~rc1-2) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Dec 30 08:40:09 UTC 2024. Universal Time is now: Mon Dec 30 08:40:09 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpython3.13-minimal:arm64 (3.13.1-2) ... Setting up autotools-dev (20220109.1) ... Setting up libunbound8:arm64 (1.22.0-1) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-3) ... Setting up libexpat1-dev:arm64 (2.6.4-1) ... Setting up libncurses6:arm64 (6.5-2+b1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libproc2-0:arm64 (2:4.0.4-6) ... Setting up comerr-dev:arm64 (2.1-1.47.2~rc1-2) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up libssl-dev:arm64 (3.3.2-2) ... Setting up autopoint (0.22.5-3) ... Setting up d-shlibs (0.109) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:arm64 (1.6.0-2) ... Setting up libnghttp3-dev:arm64 (1.6.0-2) ... Setting up ruby-webrick (1.8.1-1) ... Setting up liblzma-dev:arm64 (5.6.3-1+b1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.6-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up libtasn1-6:arm64 (4.19.0-3+b3) ... Setting up python3.13-minimal (3.13.1-2) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:arm64 (1.9.1-1) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up dos2unix (7.5.2-1+b1) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libtasn1-6-dev:arm64 (4.19.0-3+b3) ... Setting up openssl (3.3.2-2) ... Setting up libdeflate-dev:arm64 (1.22-1) ... Setting up readline-common (8.2-6) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libbrotli-dev:arm64 (1.1.0-2+b6) ... Setting up chrpath (0.18-1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libbz2-dev:arm64 (1.0.8-6) ... 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 (0.22.5-3) ... Setting up libgmp-dev:arm64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:arm64 (3.10-1+b1) ... Setting up libtool (2.4.7-8) ... Setting up libidn2-0:arm64 (2.3.7-2+b1) ... Setting up libngtcp2-dev:arm64 (1.9.1-1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libssh2-1-dev:arm64 (1.11.1-1) ... Setting up libidn2-dev:arm64 (2.3.7-2+b1) ... Setting up libjs-sphinxdoc (8.1.3-3) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-7) ... Setting up libpython3.13-stdlib:arm64 (3.13.1-2) ... Setting up libp11-kit-dev:arm64 (0.25.5-3) ... Setting up libpython3.13:arm64 (3.13.1-2) ... Setting up libgnutls30t64:arm64 (3.8.8-2) ... Setting up libgnutls-openssl27t64:arm64 (3.8.8-2) ... Setting up libnghttp2-dev:arm64 (1.64.0-1) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Setting up python3.13 (3.13.1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up bc (1.07.1-4+b1) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libldap-2.5-0:arm64 (2.5.19+dfsg-1) ... Setting up libpsl-dev:arm64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:arm64 (3.8.8-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:arm64 (1.21.3-3) ... Setting up libldap-dev:arm64 (2.5.19+dfsg-1) ... Setting up libpython3.13-dev:arm64 (3.13.1-2) ... Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.9.1-1) ... Setting up libkadm5clnt-mit12:arm64 (1.21.3-3) ... Setting up libgnutls28-dev:arm64 (3.8.8-2) ... Setting up libpython3.12-stdlib:arm64 (3.12.8-3) ... Setting up libkdb5-10t64:arm64 (1.21.3-3) ... Setting up python3.13-dev (3.13.1-2) ... Setting up python3.12 (3.12.8-3) ... Setting up libcurl3t64-gnutls:arm64 (8.11.1-1) ... Setting up debhelper (13.23) ... Setting up libngtcp2-crypto-gnutls-dev:arm64 (1.9.1-1) ... Setting up libpython3.12t64:arm64 (3.12.8-3) ... Setting up librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libkadm5srv-mit12:arm64 (1.21.3-3) ... Setting up libhts3t64:arm64 (1.20+ds-2) ... Setting up libpython3-stdlib:arm64 (3.12.8-1) ... Setting up krb5-multidev:arm64 (1.21.3-3) ... Setting up python3 (3.12.8-1) ... Setting up libpython3.12-dev:arm64 (3.12.8-3) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up samtools (1.20-3+b1) ... Setting up libkrb5-dev:arm64 (1.21.3-3) ... Setting up python3.12-dev (3.12.8-3) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up libpython3-dev:arm64 (3.12.8-1) ... 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-all (3.12.8-1) ... Setting up libcurl4-gnutls-dev:arm64 (8.11.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up libpython3-all-dev:arm64 (3.12.8-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.12.8-1) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up python3-all-dev (3.12.8-1) ... Setting up python3-setuptools (75.6.0-1) ... Setting up libhts-dev:arm64 (1.20+ds-2) ... Setting up dh-python (6.20241217) ... Setting up rake (13.2.1-1) ... Setting up libruby:arm64 (1:3.1+nmu1) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up ruby-sdbm:arm64 (1.0.0-5+b5) ... Setting up libruby3.1t64:arm64 (3.1.2-8.4) ... Setting up ruby3.1 (3.1.2-8.4) ... Setting up ruby (1:3.1+nmu1) ... Setting up yaggo (1.5.11-2) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/3884382/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3884382/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/jellyfish-2.3.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../jellyfish_2.3.1-4_source.changes dpkg-buildpackage: info: source package jellyfish dpkg-buildpackage: info: source version 2.3.1-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean debian/rules execute_after_dh_clean make[1]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' if [ -d debian/tmp_save_tests ] ; then \ mv debian/tmp_save_tests/* tests ; \ rmdir debian/tmp_save_tests ; \ fi make[1]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' debian/rules binary dh binary debian/rules override_dh_update_autotools_config make[1]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' # use python configuration from autoconf-archive mv m4/m4-ax_python_devel.m4 /tmp dh_update_autotools_config make[1]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:8: installing './compile' configure.ac:2: installing './config.guess' configure.ac:2: installing './config.sub' configure.ac:4: installing './install-sh' configure.ac:4: installing './missing' Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' dh_auto_configure -- --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3 ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3 checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for ld... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for shared library run path origin... done checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking 32-bit host C ABI... no checking for egrep -e... (cached) /usr/bin/grep -E checking for ELF binary format... yes checking for the common suffixes of directories in the library search path... lib,lib,lib checking for htslib... yes checking for samtools... /usr/bin/samtools checking for unix2dos... /usr/bin/unix2dos checking for md5sum... md5sum checking for yaggo... /usr/bin/yaggo checking for x86 cpuid output... unknown checking for x86-AVX xgetbv output... unknown checking for __int128... yes checking for std::numeric_limits<__int128>... yes checking for _NSGetExecutablePath... no checking for execinfo.h... yes checking for ext/stdio_filebuf.h... yes checking for sys/syscall.h... yes checking for sys/prctl.h... yes checking for siginfo_t.si_int... yes checking for swig... /usr/bin/swig checking SWIG version... 4.3.0 checking for SWIG library... /usr/share/swig/4.3.0 checking for python... /usr/bin/python3 checking for a version of Python >= '2.1.0'... yes checking for the sysconfig Python package... yes checking for Python include path... -I/usr/include/python3.12 checking for Python library path... -L/usr/lib/aarch64-linux-gnu -lpython3.12 checking for Python site-packages path... /usr/lib/python3.12/site-packages checking for Python platform specific site-packages path... /usr/lib/python3.12/site-packages checking python extra libraries... -ldl -lm checking python extra linking flags... -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions checking consistency of all components of python development environment... yes checking for perl... /usr/bin/perl checking for Perl prefix... /usr checking for Perl extension include path... /usr/lib/aarch64-linux-gnu/perl/5.40/CORE checking for Perl extension target directory... /usr/lib/perl/5.40.0 checking for Perl extensions C preprocessor flags... -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include checking for Perl extensions linker flags... -shared -L/usr/local/lib -fstack-protector-strong checking for posix_memalign... yes checking for aligned_alloc... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating compat.sh config.status: creating jellyfish-2.0.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_configure --sourcedirectory=swig/perl5 cd swig/perl5 && /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2" "LD=aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -lpthread" -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1 -L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -lpthread -L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu Warning (mostly harmless): No library found for -ljellyfish-2.0 Generating a Unix-style Makefile Writing Makefile for jellyfish Writing MYMETA.yml and MYMETA.json dh_auto_configure --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config running config I: pybuild base:311: python3.12 setup.py config running config mv /tmp/m4-ax_python_devel.m4 m4 make[1]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' mkdir -p debian/tmp_save_tests cp -a tests/* debian/tmp_save_tests dh_auto_build --no-parallel -- all bin/generate_sequence bin/test_all bin/fastq2sam make -j1 all bin/generate_sequence bin/test_all bin/fastq2sam make[2]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' /usr/bin/yaggo --license ./header-license -o sub_commands/count_main_cmdline.hpp sub_commands/count_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/info_main_cmdline.hpp sub_commands/info_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/dump_main_cmdline.hpp sub_commands/dump_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/histo_main_cmdline.hpp sub_commands/histo_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/stats_main_cmdline.hpp sub_commands/stats_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/merge_main_cmdline.hpp sub_commands/merge_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/bc_main_cmdline.hpp sub_commands/bc_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/query_main_cmdline.hpp sub_commands/query_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/cite_main_cmdline.hpp sub_commands/cite_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/mem_main_cmdline.hpp sub_commands/mem_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o jellyfish/generate_sequence_cmdline.hpp jellyfish/generate_sequence_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o jellyfish/fastq2sam_cmdline.hpp jellyfish/fastq2sam_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o unit_tests/test_main_cmdline.hpp unit_tests/test_main_cmdline.yaggo /usr/bin/swig -c++ -python -I./../include -o swig/python/swig_wrap.cpp swig/jellyfish.i /usr/bin/swig -c++ -perl5 -I./../include -o swig/perl5/swig_wrap.cpp swig/jellyfish.i make all-am make[3]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time 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>/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.40.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -Wl,-rpath -Wl,/build/reproducible-path/jellyfish-2.3.1/.libs -lpthread ./.libs/libjellyfish-2.0.so -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib 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-I/usr/include/python3.12 -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c swig/python/swig_wrap.cpp -o swig/python/swig_python__dna_jellyfish_la-swig_wrap.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.12/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la libtool: link: g++ 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-I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c -o unit_tests/bin_test_all-test_offsets_key_value.o `test -f 'unit_tests/test_offsets_key_value.cc' || echo './'`unit_tests/test_offsets_key_value.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c -o unit_tests/bin_test_all-test_simple_circular_buffer.o `test -f 'unit_tests/test_simple_circular_buffer.cc' || echo './'`unit_tests/test_simple_circular_buffer.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c -o unit_tests/bin_test_all-test_rectangular_binary_matrix.o `test -f 'unit_tests/test_rectangular_binary_matrix.cc' || echo './'`unit_tests/test_rectangular_binary_matrix.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time 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unit_tests/bin_test_all-test_large_hash_array.o `test -f 'unit_tests/test_large_hash_array.cc' || echo './'`unit_tests/test_large_hash_array.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o `test -f 'unit_tests/test_mer_overlap_sequence_parser.cc' || echo './'`unit_tests/test_mer_overlap_sequence_parser.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c -o unit_tests/bin_test_all-test_file_header.o `test -f 'unit_tests/test_file_header.cc' || echo './'`unit_tests/test_file_header.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_iterator.o `test -f 'unit_tests/test_mer_iterator.cc' || echo './'`unit_tests/test_mer_iterator.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c -o unit_tests/bin_test_all-test_hash_counter.o `test -f 'unit_tests/test_hash_counter.cc' || echo './'`unit_tests/test_hash_counter.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 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-DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c -o unit_tests/bin_test_all-test_token_ring.o `test -f 'unit_tests/test_token_ring.cc' || echo './'`unit_tests/test_token_ring.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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unit_tests/gtest/src/gtest-all.cc -fPIC -DPIC -o unit_tests/gtest/src/.libs/libgtest_la-gtest-all.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c unit_tests/gtest/src/gtest-all.cc -o unit_tests/gtest/src/libgtest_la-gtest-all.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -pthread -L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -lhts -R/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o libgtest.la unit_tests/gtest/src/libgtest_la-gtest-all.lo libtool: link: ar cr .libs/libgtest.a unit_tests/gtest/src/.libs/libgtest_la-gtest-all.o libtool: link: ranlib .libs/libgtest.a libtool: link: ( cd ".libs" && rm -f "libgtest.la" && ln -s "../libgtest.la" "libgtest.la" ) /bin/bash ./libtool --tag=CXX --mode=link g++ -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -pthread -L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -lhts -R/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o bin/test_all unit_tests/bin_test_all-test_main.o unit_tests/bin_test_all-test_misc.o unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_rectangular_binary_matrix.o unit_tests/bin_test_all-test_mer_dna.o unit_tests/bin_test_all-test_large_hash_array.o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o unit_tests/bin_test_all-test_file_header.o unit_tests/bin_test_all-test_mer_iterator.o unit_tests/bin_test_all-test_hash_counter.o unit_tests/bin_test_all-test_mer_heap.o unit_tests/bin_test_all-test_stream_iterator.o unit_tests/bin_test_all-test_token_ring.o unit_tests/bin_test_all-test_text_dumper.o unit_tests/bin_test_all-test_dumpers.o unit_tests/bin_test_all-test_mapped_file.o unit_tests/bin_test_all-test_int128.o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o unit_tests/bin_test_all-test_whole_sequence_parser.o unit_tests/bin_test_all-test_allocators_mmap.o unit_tests/bin_test_all-test_cooperative_pool2.o unit_tests/bin_test_all-test_generator_manager.o unit_tests/bin_test_all-test_atomic_bits_array.o unit_tests/bin_test_all-test_stdio_filebuf.o jellyfish/bin_test_all-backtrace.o libgtest.la libjellyfish-2.0.la libtool: link: g++ -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/test_all unit_tests/bin_test_all-test_main.o unit_tests/bin_test_all-test_misc.o unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_rectangular_binary_matrix.o unit_tests/bin_test_all-test_mer_dna.o unit_tests/bin_test_all-test_large_hash_array.o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o unit_tests/bin_test_all-test_file_header.o unit_tests/bin_test_all-test_mer_iterator.o unit_tests/bin_test_all-test_hash_counter.o unit_tests/bin_test_all-test_mer_heap.o unit_tests/bin_test_all-test_stream_iterator.o unit_tests/bin_test_all-test_token_ring.o unit_tests/bin_test_all-test_text_dumper.o unit_tests/bin_test_all-test_dumpers.o unit_tests/bin_test_all-test_mapped_file.o unit_tests/bin_test_all-test_int128.o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o unit_tests/bin_test_all-test_whole_sequence_parser.o unit_tests/bin_test_all-test_allocators_mmap.o unit_tests/bin_test_all-test_cooperative_pool2.o unit_tests/bin_test_all-test_generator_manager.o unit_tests/bin_test_all-test_atomic_bits_array.o unit_tests/bin_test_all-test_stdio_filebuf.o jellyfish/bin_test_all-backtrace.o -L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu ./.libs/libgtest.a -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c -o jellyfish/fastq2sam.o jellyfish/fastq2sam.cc /bin/bash ./libtool --tag=CXX --mode=link g++ -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -pthread -L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -lhts -R/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o bin/fastq2sam jellyfish/fastq2sam.o libjellyfish-2.0.la libtool: link: g++ -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/fastq2sam jellyfish/fastq2sam.o -L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu make[2]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' dh_auto_install -- install-data make -j1 install DESTDIR=/build/reproducible-path/jellyfish-2.3.1/debian/tmp AM_UPDATE_INFO_DIR=no install-data make[2]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' make install-am make[3]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' make[4]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/bin' libtool: warning: 'libjellyfish-2.0.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c bin/.libs/jellyfish /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/bin/jellyfish /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1; /bin/sh "/build/reproducible-path/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.40.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/reproducible-path/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1; /bin/sh "/build/reproducible-path/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.12/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/reproducible-path/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' make[4]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' make[3]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1; /bin/sh "/build/reproducible-path/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.40.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/reproducible-path/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1; /bin/sh "/build/reproducible-path/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.12/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/reproducible-path/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' make[2]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' dh_auto_build --sourcedirectory=swig/perl5 cd swig/perl5 && make -j12 make[2]: Entering directory '/build/reproducible-path/jellyfish-2.3.1/swig/perl5' Running Mkbootstrap for jellyfish () g++ -c -std=c++0x -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.0.1\" -DXS_VERSION=\"0.0.1\" -fPIC "-I/usr/lib/aarch64-linux-gnu/perl/5.40/CORE" swig_wrap.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ chmod 644 "jellyfish.bs" "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- jellyfish.bs blib/arch/auto/jellyfish/jellyfish.bs 644 rm -f blib/arch/auto/jellyfish/jellyfish.so aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -lpthread -shared -L/usr/local/lib -fstack-protector-strong swig_wrap.o -o blib/arch/auto/jellyfish/jellyfish.so \ -lpthread \ chmod 755 blib/arch/auto/jellyfish/jellyfish.so make[2]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1/swig/perl5' dh_auto_build --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py build build_ext -L/build/reproducible-path/jellyfish-2.3.1/.libs running build running build_py copying dna_jellyfish.py -> /build/reproducible-path/jellyfish-2.3.1/.pybuild/cpython3_3.13_dna_jellyfish/build running build_ext building '_dna_jellyfish' extension creating build/temp.linux-aarch64-cpython-313 aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1 -I/usr/include/python3.13 -c swig_wrap.cpp -o build/temp.linux-aarch64-cpython-313/swig_wrap.o -std=c++0x aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -lpthread -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/swig_wrap.o -L-L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -L/build/reproducible-path/jellyfish-2.3.1/.libs -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -lpthread -o /build/reproducible-path/jellyfish-2.3.1/.pybuild/cpython3_3.13_dna_jellyfish/build/_dna_jellyfish.cpython-313-aarch64-linux-gnu.so -Wl,-rpath,-L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu I: pybuild base:311: /usr/bin/python3 setup.py build build_ext -L/build/reproducible-path/jellyfish-2.3.1/.libs running build running build_py copying dna_jellyfish.py -> /build/reproducible-path/jellyfish-2.3.1/.pybuild/cpython3_3.12_dna_jellyfish/build running build_ext building '_dna_jellyfish' extension creating build/temp.linux-aarch64-cpython-312 aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1 -I/usr/include/python3.12 -c swig_wrap.cpp -o build/temp.linux-aarch64-cpython-312/swig_wrap.o -std=c++0x aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -lpthread -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/swig_wrap.o -L-L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -L/build/reproducible-path/jellyfish-2.3.1/.libs -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -lpthread -o /build/reproducible-path/jellyfish-2.3.1/.pybuild/cpython3_3.12_dna_jellyfish/build/_dna_jellyfish.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,-L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' if ! dh_auto_test \ ; then echo "E: tests failed, ./test-suite.log follows:" \ ; cat ./test-suite.log \ ; echo "E: end of ./test-suite.log after test failure." \ ; exit 1 \ ; fi make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' make check-am make[3]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' make bin/generate_sequence bin/fastq2sam bin/test_all libgtest.la libgtest_main.la make[4]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' make[4]: 'bin/generate_sequence' is up to date. make[4]: 'bin/fastq2sam' is up to date. make[4]: 'bin/test_all' is up to date. make[4]: 'libgtest.la' is up to date. /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c -o unit_tests/gtest/src/libgtest_main_la-gtest_main.lo `test -f 'unit_tests/gtest/src/gtest_main.cc' || echo './'`unit_tests/gtest/src/gtest_main.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c unit_tests/gtest/src/gtest_main.cc -fPIC -DPIC -o unit_tests/gtest/src/.libs/libgtest_main_la-gtest_main.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c unit_tests/gtest/src/gtest_main.cc -o unit_tests/gtest/src/libgtest_main_la-gtest_main.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -pthread -L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -lhts -R/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o libgtest_main.la unit_tests/gtest/src/libgtest_main_la-gtest_main.lo libgtest.la libtool: link: (cd .libs/libgtest_main.lax/libgtest.a && ar x "/build/reproducible-path/jellyfish-2.3.1/./.libs/libgtest.a") libtool: link: ar cr .libs/libgtest_main.a unit_tests/gtest/src/.libs/libgtest_main_la-gtest_main.o .libs/libgtest_main.lax/libgtest.a/libgtest_la-gtest-all.o libtool: link: ranlib .libs/libgtest_main.a libtool: link: rm -fr .libs/libgtest_main.lax libtool: link: ( cd ".libs" && rm -f "libgtest_main.la" && ln -s "../libgtest_main.la" "libgtest_main.la" ) make[4]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' make check-TESTS make[4]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' make[5]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' SKIP: tests/big.sh PASS: tests/generate_sequence.sh SKIP: tests/swig_ruby.sh PASS: tests/swig_python.sh PASS: tests/subset_hashing.sh PASS: tests/bloom_filter.sh PASS: tests/bloom_counter.sh PASS: tests/sam.sh PASS: tests/multi_file.sh PASS: tests/swig_perl.sh PASS: tests/large_key.sh PASS: tests/small_mers.sh PASS: tests/merge.sh PASS: tests/parallel_hashing.sh PASS: unit_tests/unit_tests.sh ============================================================================ Testsuite summary for jellyfish 2.3.1 ============================================================================ # TOTAL: 15 # PASS: 13 # SKIP: 2 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' make[4]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' make[3]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' make[2]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' make[1]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' chrpath --delete bin/.libs/* dh_auto_install -- install-data make -j1 install DESTDIR=/build/reproducible-path/jellyfish-2.3.1/debian/tmp AM_UPDATE_INFO_DIR=no install-data make[2]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' make install-am make[3]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' make[4]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/bin' libtool: warning: 'libjellyfish-2.0.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c bin/.libs/jellyfish /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/bin/jellyfish /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1; /bin/sh "/build/reproducible-path/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.40.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/reproducible-path/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1; /bin/sh "/build/reproducible-path/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.12/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/reproducible-path/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' make[4]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' make[3]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1; /bin/sh "/build/reproducible-path/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.40.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/reproducible-path/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.40.0' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1; /bin/sh "/build/reproducible-path/jellyfish-2.3.1/libtool" --tag CXX --mode=relink g++ -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.12/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/reproducible-path/jellyfish-2.3.1/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' make[2]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' dh_auto_install --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py install --root /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish 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 copying dna_jellyfish.py -> /build/reproducible-path/jellyfish-2.3.1/.pybuild/cpython3_3.13_dna_jellyfish/build running build_ext running install_lib creating /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages copying /build/reproducible-path/jellyfish-2.3.1/.pybuild/cpython3_3.13_dna_jellyfish/build/dna_jellyfish.py -> /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages copying /build/reproducible-path/jellyfish-2.3.1/.pybuild/cpython3_3.13_dna_jellyfish/build/_dna_jellyfish.cpython-313-aarch64-linux-gnu.so -> /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages byte-compiling /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages/dna_jellyfish.py to dna_jellyfish.cpython-313.pyc running install_egg_info running egg_info creating dna_jellyfish.egg-info writing dna_jellyfish.egg-info/PKG-INFO writing dependency_links to dna_jellyfish.egg-info/dependency_links.txt writing top-level names to dna_jellyfish.egg-info/top_level.txt writing manifest file 'dna_jellyfish.egg-info/SOURCES.txt' reading manifest file 'dna_jellyfish.egg-info/SOURCES.txt' writing manifest file 'dna_jellyfish.egg-info/SOURCES.txt' Copying dna_jellyfish.egg-info to /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages/dna_jellyfish-0.0.1.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish 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 copying dna_jellyfish.py -> /build/reproducible-path/jellyfish-2.3.1/.pybuild/cpython3_3.12_dna_jellyfish/build running build_ext running install_lib creating /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.12/dist-packages copying /build/reproducible-path/jellyfish-2.3.1/.pybuild/cpython3_3.12_dna_jellyfish/build/dna_jellyfish.py -> /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.12/dist-packages copying /build/reproducible-path/jellyfish-2.3.1/.pybuild/cpython3_3.12_dna_jellyfish/build/_dna_jellyfish.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.12/dist-packages byte-compiling /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.12/dist-packages/dna_jellyfish.py to dna_jellyfish.cpython-312.pyc running install_egg_info running egg_info writing dna_jellyfish.egg-info/PKG-INFO writing dependency_links to dna_jellyfish.egg-info/dependency_links.txt writing top-level names to dna_jellyfish.egg-info/top_level.txt reading manifest file 'dna_jellyfish.egg-info/SOURCES.txt' writing manifest file 'dna_jellyfish.egg-info/SOURCES.txt' Copying dna_jellyfish.egg-info to /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.12/dist-packages/dna_jellyfish-0.0.1.egg-info Skipping SOURCES.txt running install_scripts dh_auto_install --sourcedirectory=swig/perl5 cd swig/perl5 && make -j12 install DESTDIR=/build/reproducible-path/jellyfish-2.3.1/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[2]: Entering directory '/build/reproducible-path/jellyfish-2.3.1/swig/perl5' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- jellyfish.bs blib/arch/auto/jellyfish/jellyfish.bs 644 Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/perl5/5.40/auto/jellyfish/jellyfish.so make[2]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1/swig/perl5' ls -l debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so -r-xr-xr-x 1 pbuilder2 pbuilder2 1228064 Dec 30 22:45 debian/tmp/usr/lib/aarch64-linux-gnu/perl5/5.40/auto/jellyfish/jellyfish.so if [ ! -e debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so ] ; then sleep 1; fi chmod +w debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so chrpath --delete debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so dh_install d-shlibmove --commit \ --multiarch \ --devunversioned \ --movedev "debian/tmp/usr/include/jellyfish*/jellyfish/*.hpp" usr/include/jellyfish \ --movedev "debian/tmp/usr/include/jellyfish*/jellyfish/*.h" usr/include/jellyfish \ --movedev config.h usr/include/jellyfish \ debian/tmp/usr/lib/*/libjellyfish-*.so Library package automatic movement utility set -e install -d -m 755 debian/libjellyfish-2.0-dev/usr/lib/aarch64-linux-gnu install -d -m 755 debian/libjellyfish-2.0-2/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a debian/libjellyfish-2.0-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.la debian/libjellyfish-2.0-dev/usr/lib/aarch64-linux-gnu || true mv debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so debian/libjellyfish-2.0-dev/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2 debian/libjellyfish-2.0-2/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2.0.0 debian/libjellyfish-2.0-2/usr/lib/aarch64-linux-gnu PKGDEV=libjellyfish-2.0-dev PKGSHL=libjellyfish-2.0-2 install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish mv debian/tmp/usr/include/jellyfish*/jellyfish/*.hpp debian/libjellyfish-2.0-dev/usr/include/jellyfish install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish mv debian/tmp/usr/include/jellyfish*/jellyfish/*.h debian/libjellyfish-2.0-dev/usr/include/jellyfish install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish mv config.h debian/libjellyfish-2.0-dev/usr/include/jellyfish sed -i "/dependency_libs/ s/'.*'/''/" ./debian/libjellyfish-2.0-dev/usr/lib/aarch64-linux-gnu/*.la chrpath --delete debian/*/usr/lib/python*/dist-packages/_dna_jellyfish*.so make[1]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' dh_install debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' # Fix PACKAGE_NAME defined in config.h colliding with potential reverse # dependencies autotools invocations, per lintian warning. rm -vf debian/libjellyfish-2.0-dev/usr/include/jellyfish/config.h removed 'debian/libjellyfish-2.0-dev/usr/include/jellyfish/config.h' make[1]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_python3 dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms debian/rules override_dh_missing make[1]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' # Python files are just installed rm -rf debian/tmp/usr/lib/python3/dist-packages # Necessary Perl files are just installed rm -rf debian/tmp/usr/lib/perl/5.* dh_missing make[1]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package jellyfish-examples: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'python3-dna-jellyfish-dbgsym' in '../python3-dna-jellyfish-dbgsym_2.3.1-4_arm64.deb'. dpkg-deb: building package 'jellyfish' in '../jellyfish_2.3.1-4_arm64.deb'. dpkg-deb: building package 'jellyfish-examples' in '../jellyfish-examples_2.3.1-4_all.deb'. dpkg-deb: building package 'jellyfish-dbgsym' in '../jellyfish-dbgsym_2.3.1-4_arm64.deb'. dpkg-deb: building package 'libjellyfish-2.0-2' in '../libjellyfish-2.0-2_2.3.1-4_arm64.deb'. dpkg-deb: building package 'libjellyfish-2.0-dev' in '../libjellyfish-2.0-dev_2.3.1-4_arm64.deb'. dpkg-deb: building package 'libjellyfish-2.0-2-dbgsym' in '../libjellyfish-2.0-2-dbgsym_2.3.1-4_arm64.deb'. dpkg-deb: building package 'libjellyfish-perl' in '../libjellyfish-perl_2.3.1-4_arm64.deb'. dpkg-deb: building package 'python3-dna-jellyfish' in '../python3-dna-jellyfish_2.3.1-4_arm64.deb'. dpkg-deb: building package 'libjellyfish-perl-dbgsym' in '../libjellyfish-perl-dbgsym_2.3.1-4_arm64.deb'. dpkg-genbuildinfo --build=binary -O../jellyfish_2.3.1-4_arm64.buildinfo dpkg-genchanges --build=binary -O../jellyfish_2.3.1-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3884382/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3884382/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3884382 and its subdirectories I: Current time: Mon Dec 30 22:48:08 +14 2024 I: pbuilder-time-stamp: 1735548488