I: pbuilder: network access will be disabled during build I: Current time: Mon Jun 9 23:32:57 +14 2025 I: pbuilder-time-stamp: 1749461577 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [jellyfish_2.3.1-3.dsc] I: copying [./jellyfish_2.3.1.orig.tar.gz] I: copying [./jellyfish_2.3.1-3.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Mar 19 17:22:40 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./jellyfish_2.3.1-3.dsc: no acceptable signature found 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_2.3.1-3.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/1735300/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-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 Jun 9 09:33 /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/1735300/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1735300/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]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.21(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=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=4683257f115a45c9ad0f72a27704e412 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=1735300 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.qcV1zMFJ/pbuilderrc_xITK --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qcV1zMFJ/b2 --logfile b2/build.log jellyfish_2.3.1-3.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 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 5 14:47 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1735300/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 ... 19743 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} 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} libarchive-zip-perl{a} libbrotli1{a} libbsd0{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libedit2{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} librtmp1{a} libruby{a} libruby3.1t64{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-all{a} python3-all-dev{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} python3.12{a} python3.12-dev{a} python3.12-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: curl fonts-lato javascript-common krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget zip 0 packages upgraded, 122 newly installed, 0 to remove and 0 not upgraded. Need to get 64.0 MB of archives. After unpacking 280 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-3 [255 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 14 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.11.8-1 [27.4 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.3-1 [802 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.3-1 [1931 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-4 [61.7 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-4 [869 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.2.1-3 [1324 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 architecture-properties arm64 0.1.1+b1 [1880 B] Get: 32 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 bc arm64 1.07.1-4 [101 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 chrpath arm64 0.16-2+b1 [16.0 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 d-shlibs all 0.106 [10.9 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 47 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 python3-distutils all 3.12.3-1 [131 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 68.1.2-2 [468 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20240422 [107 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 dos2unix arm64 7.5.2-1 [515 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.1~rc2-1 [22.5 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.20.1-6+b1 [33.0 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.20.1-6+b1 [80.5 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 67 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.20.1-6+b1 [315 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.20.1-6+b1 [124 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-6 [20.1 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-6 [55.3 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.17+dfsg-1 [173 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.61.0-1+b1 [71.0 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.7.1-3 [405 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libcurl4-gnutls-dev arm64 8.7.1-3 [523 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libdeflate-dev arm64 1.20-1 [50.5 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20230828-1+b1 [89.1 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libexpat1-dev arm64 2.6.2-1 [278 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.0-1+b1 [71.6 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.19+ds-1.1+b1 [413 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 liblzma-dev arm64 5.6.1+really5.4.5-1 [289 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1 [915 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libhts-dev arm64 1.19+ds-1.1+b1 [1604 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libjs-sphinxdoc all 7.2.6-6 [150 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.4+20240414-1 [95.6 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-1+b2 [35.3 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libpython3.11t64 arm64 3.11.9-1 [1814 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libpython3.11-dev arm64 3.11.9-1 [4358 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libpython3-dev arm64 3.11.8-1 [9564 B] Get: 95 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.3-1 [1889 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libpython3.12t64 arm64 3.12.3-1 [1948 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libpython3.12-dev arm64 3.12.3-1 [4745 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libpython3-all-dev arm64 3.11.8-1 [1072 B] Get: 99 http://deb.debian.org/debian trixie/main arm64 rubygems-integration all 1.18 [6704 B] Get: 100 http://deb.debian.org/debian trixie/main arm64 ruby3.1 arm64 3.1.2-8.3 [664 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 ruby arm64 1:3.1+nmu1 [5584 B] Get: 103 http://deb.debian.org/debian trixie/main arm64 rake all 13.0.6-3 [83.9 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 ruby-sdbm arm64 1.0.0-5+b4 [14.6 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libyaml-0-2 arm64 0.2.5-1+b1 [49.0 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libruby3.1t64 arm64 3.1.2-8.3 [5254 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libruby arm64 1:3.1+nmu1 [4664 B] Get: 111 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-1+b2 [29.3 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-1+b2 [26.2 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.3-1 [659 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 python3-all arm64 3.11.8-1 [1056 B] Get: 115 http://deb.debian.org/debian trixie/main arm64 python3.11-dev arm64 3.11.9-1 [501 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 python3-dev arm64 3.11.8-1 [26.1 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 python3.12-dev arm64 3.12.3-1 [499 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 python3-all-dev arm64 3.11.8-1 [1072 B] Get: 119 http://deb.debian.org/debian trixie/main arm64 samtools arm64 1.19.2-1+b1 [617 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 swig arm64 4.2.1-1 [1350 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 time arm64 1.9-0.2 [50.6 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 yaggo all 1.5.11-1 [21.3 kB] Fetched 64.0 MB in 1s (92.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19743 files and directories currently installed.) Preparing to unpack .../autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package libpython3.11-minimal:arm64. Preparing to unpack .../libpython3.11-minimal_3.11.9-1_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.9-1) ... Selecting previously unselected package libexpat1:arm64. 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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 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_arm64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... 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 ... 22233 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_arm64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:arm64. Preparing to unpack .../001-libpython3.12-minimal_3.12.3-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../002-python3.12-minimal_3.12.3-1_arm64.deb ... Unpacking python3.12-minimal (3.12.3-1) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../003-libproc2-0_2%3a4.0.4-4_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../004-procps_2%3a4.0.4-4_arm64.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../005-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package openssl. Preparing to unpack .../006-openssl_3.2.1-3_arm64.deb ... Unpacking openssl (3.2.1-3) ... 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Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../038-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../039-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../040-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../041-python3-pkg-resources_68.1.2-2_all.deb ... Unpacking python3-pkg-resources (68.1.2-2) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../042-python3-lib2to3_3.12.3-1_all.deb ... Unpacking python3-lib2to3 (3.12.3-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../043-python3-distutils_3.12.3-1_all.deb ... 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Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../050-libkrb5support0_1.20.1-6+b1_arm64.deb ... Unpacking libkrb5support0:arm64 (1.20.1-6+b1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../051-libk5crypto3_1.20.1-6+b1_arm64.deb ... Unpacking libk5crypto3:arm64 (1.20.1-6+b1) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../052-libkeyutils1_1.6.3-3_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../053-libkrb5-3_1.20.1-6+b1_arm64.deb ... Unpacking libkrb5-3:arm64 (1.20.1-6+b1) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../054-libgssapi-krb5-2_1.20.1-6+b1_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.20.1-6+b1) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../055-libsasl2-modules-db_2.1.28+dfsg1-6_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../056-libsasl2-2_2.1.28+dfsg1-6_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../057-libldap-2.5-0_2.5.17+dfsg-1_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.17+dfsg-1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../058-libnghttp2-14_1.61.0-1+b1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.61.0-1+b1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../059-libpsl5t64_0.21.2-1.1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../060-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../061-libssh2-1t64_1.11.0-4.1+b2_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.0-4.1+b2) ... Selecting previously unselected package libcurl3t64-gnutls:arm64. Preparing to unpack .../062-libcurl3t64-gnutls_8.7.1-3_arm64.deb ... Unpacking libcurl3t64-gnutls:arm64 (8.7.1-3) ... Selecting previously unselected package libcurl4-gnutls-dev:arm64. Preparing to unpack .../063-libcurl4-gnutls-dev_8.7.1-3_arm64.deb ... Unpacking libcurl4-gnutls-dev:arm64 (8.7.1-3) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../064-libdeflate0_1.20-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.20-1) ... Selecting previously unselected package libdeflate-dev:arm64. Preparing to unpack .../065-libdeflate-dev_1.20-1_arm64.deb ... Unpacking libdeflate-dev:arm64 (1.20-1) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../066-libedit2_3.1-20230828-1+b1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20230828-1+b1) ... Selecting previously unselected package libexpat1-dev:arm64. Preparing to unpack .../067-libexpat1-dev_2.6.2-1_arm64.deb ... Unpacking libexpat1-dev:arm64 (2.6.2-1) ... Selecting previously unselected package libhtscodecs2:arm64. Preparing to unpack .../068-libhtscodecs2_1.6.0-1+b1_arm64.deb ... Unpacking libhtscodecs2:arm64 (1.6.0-1+b1) ... Selecting previously unselected package libhts3t64:arm64. Preparing to unpack .../069-libhts3t64_1.19+ds-1.1+b1_arm64.deb ... Unpacking libhts3t64:arm64 (1.19+ds-1.1+b1) ... Selecting previously unselected package liblzma-dev:arm64. Preparing to unpack .../070-liblzma-dev_5.6.1+really5.4.5-1_arm64.deb ... Unpacking liblzma-dev:arm64 (5.6.1+really5.4.5-1) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../071-zlib1g-dev_1%3a1.3.dfsg-3.1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3.1) ... Selecting previously unselected package libhts-dev:arm64. Preparing to unpack .../072-libhts-dev_1.19+ds-1.1+b1_arm64.deb ... Unpacking libhts-dev:arm64 (1.19+ds-1.1+b1) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../073-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../074-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../075-libjs-sphinxdoc_7.2.6-6_all.deb ... Unpacking libjs-sphinxdoc (7.2.6-6) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../076-libncurses6_6.4+20240414-1_arm64.deb ... Unpacking libncurses6:arm64 (6.4+20240414-1) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../077-libpkgconf3_1.8.1-1+b2_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-1+b2) ... Selecting previously unselected package libpython3.11t64:arm64. Preparing to unpack .../078-libpython3.11t64_3.11.9-1_arm64.deb ... Unpacking libpython3.11t64:arm64 (3.11.9-1) ... Selecting previously unselected package libpython3.11-dev:arm64. Preparing to unpack .../079-libpython3.11-dev_3.11.9-1_arm64.deb ... Unpacking libpython3.11-dev:arm64 (3.11.9-1) ... Selecting previously unselected package libpython3-dev:arm64. Preparing to unpack .../080-libpython3-dev_3.11.8-1_arm64.deb ... Unpacking libpython3-dev:arm64 (3.11.8-1) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../081-libpython3.12-stdlib_3.12.3-1_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.3-1) ... Selecting previously unselected package libpython3.12t64:arm64. Preparing to unpack .../082-libpython3.12t64_3.12.3-1_arm64.deb ... Unpacking libpython3.12t64:arm64 (3.12.3-1) ... Selecting previously unselected package libpython3.12-dev:arm64. Preparing to unpack .../083-libpython3.12-dev_3.12.3-1_arm64.deb ... Unpacking libpython3.12-dev:arm64 (3.12.3-1) ... Selecting previously unselected package libpython3-all-dev:arm64. Preparing to unpack .../084-libpython3-all-dev_3.11.8-1_arm64.deb ... Unpacking libpython3-all-dev:arm64 (3.11.8-1) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../085-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../086-ruby3.1_3.1.2-8.3_arm64.deb ... Unpacking ruby3.1 (3.1.2-8.3) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../087-ruby-rubygems_3.4.20-1_all.deb ... Unpacking ruby-rubygems (3.4.20-1) ... Selecting previously unselected package ruby. Preparing to unpack .../088-ruby_1%3a3.1+nmu1_arm64.deb ... Unpacking ruby (1:3.1+nmu1) ... Selecting previously unselected package rake. Preparing to unpack .../089-rake_13.0.6-3_all.deb ... Unpacking rake (13.0.6-3) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../090-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../091-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../092-ruby-xmlrpc_0.3.2-2_all.deb ... Unpacking ruby-xmlrpc (0.3.2-2) ... Selecting previously unselected package ruby-sdbm:arm64. Preparing to unpack .../093-ruby-sdbm_1.0.0-5+b4_arm64.deb ... Unpacking ruby-sdbm:arm64 (1.0.0-5+b4) ... Selecting previously unselected package libyaml-0-2:arm64. Preparing to unpack .../094-libyaml-0-2_0.2.5-1+b1_arm64.deb ... Unpacking libyaml-0-2:arm64 (0.2.5-1+b1) ... Selecting previously unselected package libruby3.1t64:arm64. Preparing to unpack .../095-libruby3.1t64_3.1.2-8.3_arm64.deb ... Unpacking libruby3.1t64:arm64 (3.1.2-8.3) ... Selecting previously unselected package libruby:arm64. Preparing to unpack .../096-libruby_1%3a3.1+nmu1_arm64.deb ... Unpacking libruby:arm64 (1:3.1+nmu1) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../097-pkgconf-bin_1.8.1-1+b2_arm64.deb ... Unpacking pkgconf-bin (1.8.1-1+b2) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../098-pkgconf_1.8.1-1+b2_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-1+b2) ... Selecting previously unselected package python3.12. Preparing to unpack .../099-python3.12_3.12.3-1_arm64.deb ... Unpacking python3.12 (3.12.3-1) ... Selecting previously unselected package python3-all. Preparing to unpack .../100-python3-all_3.11.8-1_arm64.deb ... Unpacking python3-all (3.11.8-1) ... Selecting previously unselected package python3.11-dev. Preparing to unpack .../101-python3.11-dev_3.11.9-1_arm64.deb ... Unpacking python3.11-dev (3.11.9-1) ... Selecting previously unselected package python3-dev. Preparing to unpack .../102-python3-dev_3.11.8-1_arm64.deb ... Unpacking python3-dev (3.11.8-1) ... Selecting previously unselected package python3.12-dev. Preparing to unpack .../103-python3.12-dev_3.12.3-1_arm64.deb ... Unpacking python3.12-dev (3.12.3-1) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../104-python3-all-dev_3.11.8-1_arm64.deb ... Unpacking python3-all-dev (3.11.8-1) ... Selecting previously unselected package samtools. Preparing to unpack .../105-samtools_1.19.2-1+b1_arm64.deb ... Unpacking samtools (1.19.2-1+b1) ... Selecting previously unselected package swig. Preparing to unpack .../106-swig_4.2.1-1_arm64.deb ... Unpacking swig (4.2.1-1) ... Selecting previously unselected package time. Preparing to unpack .../107-time_1.9-0.2_arm64.deb ... Unpacking time (1.9-0.2) ... Selecting previously unselected package yaggo. Preparing to unpack .../108-yaggo_1.5.11-1_all.deb ... Unpacking yaggo (1.5.11-1) ... Setting up libhtscodecs2:arm64 (1.6.0-1+b1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up time (1.9-0.2) ... Setting up libkeyutils1:arm64 (1.6.3-3) ... Setting up swig (4.2.1-1) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.5-1+b1) ... Setting up architecture-properties:arm64 (0.1.1+b1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:arm64 (1.1.0-2+b3) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up libpython3.12-minimal:arm64 (3.12.3-1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1) ... Setting up libnghttp2-14:arm64 (1.61.0-1+b1) ... Setting up libdeflate0:arm64 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up autoconf-archive (20220903-3) ... Setting up libcom-err2:arm64 (1.47.1~rc2-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up libkrb5support0:arm64 (1.20.1-6+b1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Jun 9 09:33:42 UTC 2025. Universal Time is now: Mon Jun 9 09:33:42 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:arm64 (1.8.1-1+b2) ... Setting up libexpat1-dev:arm64 (2.6.2-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:arm64 (6.4+20240414-1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libproc2-0:arm64 (2:4.0.4-4) ... Setting up autopoint (0.21-14) ... Setting up d-shlibs (0.106) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libk5crypto3:arm64 (1.20.1-6+b1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-6) ... Setting up autoconf (2.71-3) ... Setting up ruby-webrick (1.8.1-1) ... Setting up liblzma-dev:arm64 (5.6.1+really5.4.5-1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-4) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up libkrb5-3:arm64 (1.20.1-6+b1) ... Setting up dos2unix (7.5.2-1) ... Setting up libssh2-1t64:arm64 (1.11.0-4.1+b2) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:arm64 (0.12.2-1) ... Setting up libdeflate-dev:arm64 (1.20-1) ... Setting up readline-common (8.2-4) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up chrpath (0.16-2+b1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 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 (1.13.1-1) ... Setting up python3.12-minimal (3.12.3-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libedit2:arm64 (3.1-20230828-1+b1) ... Setting up libldap-2.5-0:arm64 (2.5.17+dfsg-1) ... Setting up pkgconf:arm64 (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libgssapi-krb5-2:arm64 (1.20.1-6+b1) ... Setting up libjs-sphinxdoc (7.2.6-6) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up libpython3.12-stdlib:arm64 (3.12.3-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libpython3.11t64:arm64 (3.11.9-1) ... Setting up libcurl3t64-gnutls:arm64 (8.7.1-3) ... Setting up bc (1.07.1-4) ... Setting up rubygems-integration (1.18) ... Setting up libcurl4-gnutls-dev:arm64 (8.7.1-3) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3.12t64:arm64 (3.12.3-1) ... Setting up libpython3.11-dev:arm64 (3.11.9-1) ... Setting up libhts3t64:arm64 (1.19+ds-1.1+b1) ... Setting up libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libpython3-dev:arm64 (3.11.8-1) ... Setting up python3.11-dev (3.11.9-1) ... Setting up libhts-dev:arm64 (1.19+ds-1.1+b1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up libpython3.12-dev:arm64 (3.12.3-1) ... Setting up samtools (1.19.2-1+b1) ... Setting up libpython3-all-dev:arm64 (3.11.8-1) ... Setting up python3.12-dev (3.12.3-1) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up python3-setuptools (68.1.2-2) ... Setting up python3-all (3.11.8-1) ... Setting up python3-dev (3.11.8-1) ... Setting up dh-python (6.20240422) ... Setting up python3-all-dev (3.11.8-1) ... Setting up rake (13.0.6-3) ... Setting up ruby-sdbm:arm64 (1.0.0-5+b4) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up libruby3.1t64:arm64 (3.1.2-8.3) ... Setting up ruby3.1 (3.1.2-8.3) ... Setting up libruby:arm64 (1:3.1+nmu1) ... Setting up ruby (1:3.1+nmu1) ... Setting up yaggo (1.5.11-1) ... Processing triggers for libc-bin (2.38-7) ... Processing triggers for ca-certificates (20240203) ... 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/1735300/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/1735300/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_2.3.1-3_source.changes dpkg-buildpackage: info: source package jellyfish dpkg-buildpackage: info: source version 2.3.1-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe 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 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... 4.2.1 checking for SWIG library... /usr/share/swig/4.2.1 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/python3.11 checking for Python library path... -L/usr/lib/aarch64-linux-gnu -lpython3.11 checking for Python site-packages path... /usr/lib/python3.11/site-packages checking for Python platform specific site-packages path... /usr/lib/python3.11/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/5.38/CORE checking for Perl extension target directory... /usr/lib/perl/5.38.0 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: python3.12 setup.py config running config I: pybuild base:311: python3.11 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 -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 sub_commands/jellyfish.o sub_commands/jellyfish.cc 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 sub_commands/count_main.o sub_commands/count_main.cc 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 sub_commands/info_main.o sub_commands/info_main.cc 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 sub_commands/dump_main.o sub_commands/dump_main.cc 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 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-Werror=format-security -mbranch-protection=standard -Wno-nonnull -c -o sub_commands/merge_main.o sub_commands/merge_main.cc 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 sub_commands/bc_main.o sub_commands/bc_main.cc 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 sub_commands/query_main.o sub_commands/query_main.cc g++ 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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_main.o `test -f 'unit_tests/test_main.cc' || echo './'`unit_tests/test_main.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 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-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 -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_dna.o `test -f 'unit_tests/test_mer_dna.cc' || echo './'`unit_tests/test_mer_dna.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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unit_tests/bin_test_all-test_stream_iterator.o `test -f 'unit_tests/test_stream_iterator.cc' || echo './'`unit_tests/test_stream_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_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 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-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/bin_test_all-backtrace.o `test -f 'jellyfish/backtrace.cc' || echo './'`jellyfish/backtrace.cc /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 -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 -o unit_tests/gtest/src/libgtest_la-gtest-all.lo `test -f 'unit_tests/gtest/src/gtest-all.cc' || echo './'`unit_tests/gtest/src/gtest-all.cc 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 -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/5.38.0' /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/5.38.0' 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/5.38.0 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/13/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/13/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/13 -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/13/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/13/../../../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/5.38.0/jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.38.0 && { 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/5.38.0 && { 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/5.38.0/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/5.38.0/jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.38.0/jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.38.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.38.0' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.38.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.38.0' /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/python3.11/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/python3.11/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/python3.11/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/13/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/13/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/13 -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/13/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/13/../../../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/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.11/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/python3.11/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/python3.11/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/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.11/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/5.38.0' /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/5.38.0' 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/5.38.0 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/13/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/13/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/13 -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/13/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/13/../../../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/5.38.0/jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.38.0 && { 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/5.38.0 && { 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/5.38.0/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/5.38.0/jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.38.0/jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.38.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.38.0' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.38.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.38.0' /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/python3.11/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/python3.11/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/python3.11/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/13/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/13/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/13 -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/13/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/13/../../../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/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.11/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/python3.11/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/python3.11/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/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.11/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/5.38/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/python3.12 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 creating build/temp.linux-aarch64-cpython-312 aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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 -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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -lpthread -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 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 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_3.11_dna_jellyfish/build running build_ext building '_dna_jellyfish' extension creating build/temp.linux-aarch64-cpython-311 aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fPIC -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1 -I/usr/include/python3.11 -c swig_wrap.cpp -o build/temp.linux-aarch64-cpython-311/swig_wrap.o -std=c++0x cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lpthread -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 build/temp.linux-aarch64-cpython-311/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_3.11_dna_jellyfish/build/_dna_jellyfish.cpython-311-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/subset_hashing.sh PASS: tests/bloom_filter.sh PASS: tests/swig_perl.sh PASS: tests/bloom_counter.sh PASS: tests/sam.sh PASS: tests/multi_file.sh PASS: tests/swig_python.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/5.38.0' /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/5.38.0' 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/5.38.0 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/13/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/13/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/13 -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/13/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/13/../../../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/5.38.0/jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.38.0 && { 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/5.38.0 && { 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/5.38.0/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/5.38.0/jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.38.0/jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.38.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.38.0' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.38.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.38.0' /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/python3.11/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/python3.11/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/python3.11/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/13/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/13/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/13 -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/13/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/13/../../../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/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.11/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/python3.11/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/python3.11/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/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.11/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/5.38.0' /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/5.38.0' 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/5.38.0 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/13/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/13/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/13 -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/13/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/13/../../../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/5.38.0/jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.38.0 && { 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/5.38.0 && { 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/5.38.0/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/5.38.0/jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.38.0/jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.38.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.38.0' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.38.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/perl/5.38.0' /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/python3.11/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/python3.11/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/python3.11/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/13/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/13/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/13 -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/13/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/13/../../../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/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.11/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/python3.11/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/python3.11/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/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/python3.11/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/python3.12 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 running build_ext running install_lib creating /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish creating /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr creating /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib creating /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.12 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.cpython-312-aarch64-linux-gnu.so -> /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 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 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/python3.12/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 running build_ext running install_lib creating /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.11 creating /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.11/dist-packages copying /build/reproducible-path/jellyfish-2.3.1/.pybuild/cpython3_3.11_dna_jellyfish/build/_dna_jellyfish.cpython-311-aarch64-linux-gnu.so -> /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.11/dist-packages copying /build/reproducible-path/jellyfish-2.3.1/.pybuild/cpython3_3.11_dna_jellyfish/build/dna_jellyfish.py -> /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.11/dist-packages byte-compiling /build/reproducible-path/jellyfish-2.3.1/debian/python3-dna-jellyfish/usr/lib/python3.11/dist-packages/dna_jellyfish.py to dna_jellyfish.cpython-311.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/python3.11/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/perl5/5.38/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 1177416 Jun 9 23:42 debian/tmp/usr/lib/aarch64-linux-gnu/perl5/5.38/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 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 'libjellyfish-2.0-dev' in '../libjellyfish-2.0-dev_2.3.1-3_arm64.deb'. dpkg-deb: building package 'libjellyfish-perl' in '../libjellyfish-perl_2.3.1-3_arm64.deb'. dpkg-deb: building package 'python3-dna-jellyfish-dbgsym' in '../python3-dna-jellyfish-dbgsym_2.3.1-3_arm64.deb'. dpkg-deb: building package 'jellyfish-examples' in '../jellyfish-examples_2.3.1-3_all.deb'. dpkg-deb: building package 'jellyfish-dbgsym' in '../jellyfish-dbgsym_2.3.1-3_arm64.deb'. dpkg-deb: building package 'libjellyfish-2.0-2' in '../libjellyfish-2.0-2_2.3.1-3_arm64.deb'. dpkg-deb: building package 'libjellyfish-2.0-2-dbgsym' in '../libjellyfish-2.0-2-dbgsym_2.3.1-3_arm64.deb'. dpkg-deb: building package 'python3-dna-jellyfish' in '../python3-dna-jellyfish_2.3.1-3_arm64.deb'. dpkg-deb: building package 'libjellyfish-perl-dbgsym' in '../libjellyfish-perl-dbgsym_2.3.1-3_arm64.deb'. dpkg-deb: building package 'jellyfish' in '../jellyfish_2.3.1-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../jellyfish_2.3.1-3_arm64.buildinfo dpkg-genchanges --build=binary -O../jellyfish_2.3.1-3_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/1735300/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1735300/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/1735300 and its subdirectories I: Current time: Mon Jun 9 23:48:09 +14 2025 I: pbuilder-time-stamp: 1749462489